Putative Causes Research Articles

Characterization of neurologic disease-associated Streptococcus suis strains within the United States swine herd and use of diagnostic tools.

Streptococcus suis negatively impacts swine health, posing diagnostic and preventative challenges. S. suis can induce disease and also quietly reside on mucosal surfaces. The limited use of diagnostic tools to identify disease-associated strains and rule out differential diagnoses, alongside the complex ecology of S. suis, poses significant challenges in comprehending this important pathogen and defining pathotypes. This study evaluated 2,379 S. suis central nervous system (CNS) isolates from diagnostic submissions between 2015 and 2019. Isolates originating from submissions with histologic evidence of CNS infection (n = 1,032) were further characterized by standard and advanced diagnostic techniques. We identified 29 S. suis serotypes and 4 reclassified serotypes as putative causes of CNS disease. Among these, serotypes 1 and 7 emerged as the predominant putative causes of CNS infection (32% of submissions). Furthermore, 51 sequence types (STs), of which 15 were novel, were detected with ST1 predominating. Through whole-genome sequencing of 145 isolates, we observed that five commonly used virulence-associated genes (VAGs; epf, mrp, sly, ofs, and srtF) were not present in most disease-associated isolates, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) yielded false-positive results in 7% of isolates. These data indicate that (i) clinical signs and site of isolation alone are insufficient for defining a pathotype, (ii) S. suis serotypes and STs associated with CNS infection are more diverse than previously reported, (iii) MALDI-TOF MS may need to be supplemented with additional diagnostic tools for precise S. suis identification, and (iv) VAGs remain an unreliable means for identifying isolates associated with CNS disease.IMPORTANCEStreptococcus suis is an important and complex systemic bacterial pathogen of swine. Characterization of S. suis strains originating from pigs with histologic confirmation of neurologic disease is limited. Review of swine diagnostic submissions revealed that fewer than half of cases from which S. suis was isolated from the brain had histologic evidence of neurologic disease. This finding demonstrates that clinical signs and site of isolation alone are not sufficient for identifying a neurologic disease-associated strain. Characterization of strains originating from cases with evidence of disease using classic and advanced diagnostic techniques revealed that neurologic disease-associated strains are diverse and commonly lack genes previously associated with virulence.

Severe community-acquired pneumonia at a tertiary academic hospital in Johannesburg, South Africa

PurposeThere is a paucity of data from sub-Saharan Africa describing Severe Community Acquired Pneumonia (SCAP), a condition with significant morbidity and mortality. Materials and methodsThis was a retrospective, single-centre, observational study of consecutive patients with SCAP admitted to the ICU at Charlotte Maxeke Johannesburg Academic Hospital, in South Africa between 1 July 2007 and 31 May 2019. Pneumonia was categorised as community-acquired if there had been no hospitalization in the preceding 2 weeks. ResultsWe identified 931 patients, (median age 37 [IQR 30–48] years), with the predominant co-morbidity being HIV co-infection (77.1 %). The median CURB-65 and APACHE II scores were 3 (IQR 2–3) and 18 (IQR 14–23) respectively, and most patients had multilobar consolidation on chest X-ray. Mycobacterium tuberculosis was the most common aetiology, followed by Streptococcus pneumoniae. The latter, and Pneumocystis jirovecii were more common amongst survivors and non-survivors, respectively. ICU mortality was 50.1 % and 85 % of patients required ventilation, mostly invasive mechanical ventilation. Ventilated patients and those requiring inotropic support and/or dialysis were more likely to die. ConclusionWe have described a cohort of patients with SCAP, with a comprehensive overview of all putative microbiological causes, which to our knowledge, is the largest reported in the literature.

Abatement of the Survival Cliff in Older Adolescents and Young Adults with Acute Lymphoblastic Leukemia and Lymphoblastic Lymphoma in the United States.

Purpose: In 2018, a "survival cliff" in the United States was identified among older adolescent and young adult (AYA) patients with acute lymphoblastic leukemia (ALL) and lymphoblastic lymphoma (LBL). This study reassessed the cliff and associated putative causes. Methods: Survival data were obtained using the U.S. Surveillance Research Program, National Cancer Institute (NCI) SEER 22 Registries. Accrual data on cancer treatment trials conducted by the NCI cooperative groups and NCI-designated cancer centers were obtained from the NCI Cancer Therapy Evaluation Program. Trend and average percent changes and statistical significances were identified with the NCI Joinpoint Regression Program. Results: A previous cliff-like decrement in the survival of 17- to 20-year-olds is no longer apparent, overall and in all racial and ethnic groups. The "survival cliff" age range was coincident with a clinical trial accrual cliff, and both diminished when more clinical trials were available to, and participated in by, young adult patients. Older AYA patients of ages 30-39 had minimal improvement in clinical trial accrual and least survival gain among the AYA age group. Conclusion: The survival cliff has abated, resulting in thousands of fewer premature deaths and tens of thousands of years of life saved-a remarkable achievement. The survival improvement may be attributed to improved clinical trial availability for and recruitment and participation of AYAs on treatment trials, application of pediatric-inspired ALL treatment regimens to AYAs, expanded national health insurance for -18 to 25 year olds, improved AYA cancer services, and a national focus on AYA oncology.

The Risk of Virus Emergence in South America: A Subtle Balance Between Increasingly Favorable Conditions and a Protective Environment.

South American ecosystems host astonishing biodiversity, with potentially great richness in viruses. However, these ecosystems have not yet been the source of any widespread, epidemic viruses. Here we explore a set of putative causes that may explain this apparent paradox. We discuss that human presence in South America is recent, beginning around 14,000years ago; that few domestications of native species have occurred; and that successive immigration events associated with Old World virus introductions reduced the likelihood of spillovers and adaptation of local viruses into humans. Also, the diversity and ecological characteristics of vertebrate hosts might serve as protective factors. Moreover, although forest areas remained well preserved until recently, current brutal, sudden, and large-scale clear cuts through the forest have resulted in nearly no ecotones, which are essential for creating an adaptive gradient of microbes, hosts, and vectors. This may be temporarily preventing virus emergence. Nevertheless, the mid-term effect of such drastic changes in habitats and landscapes, coupled with explosive urbanization and climate changes, must not be overlooked by health authorities.

The emerging links between immunosenescence in innate immune system and neurocryptococcosis.

Immunosenescence refers to the age-related progressive decline of immune function contributing to the increased susceptibility to infectious diseases in older people. Neurocryptococcosis, an infectious disease of central nervous system (CNS) caused by Cryptococcus neoformans (C. Neoformans) and C. gattii, has been observed with increased frequency in aged people, as result of the reactivation of a latent infection or community acquisition. These opportunistic microorganisms belonging to kingdom of fungi are capable of surviving and replicating within macrophages. Typically, cryptococcus is expelled by vomocytosis, a non-lytic expulsive mechanism also promoted by interferon (IFN)-I, or by cell lysis. However, whereas in a first phase cryptococcal vomocytosis leads to a latent asymptomatic infection confined to the lung, an enhancement in vomocytosis, promoted by IFN-I overproduction, can be deleterious, leading the fungus to reach the blood stream and invade the CNS. Cryptococcus may not be easy to diagnose in older individuals and, if not timely treated, could be potentially lethal. Therefore, this review aims to elucidate the putative causes of the increased incidence of cryptococcal CNS infection in older people discussing in depth the mechanisms of immunosenscence potentially able to predispose to neurocryptococcosis, laying the foundations for future research. A deepest understanding of this relationship could provide new ways to improve the prevention and recognition of neurocryptococcosis in aged frail people, in order to quickly manage pharmacological interventions and to adopt further preventive measures able to reduce the main risk factors.

#2581 Cryptococcosis in kidney transplant recipients: a nationwide multicenter retrospective cohort study—CRITERE study

Abstract Background and Aims Cryptococcosis stands as the third most common invasive fungal infection in solid organ transplant recipients. Clinical management and prognosis of the disease remains largely unexplored in the context of kidney transplant recipients. Our main objective was to describe the natural history of cryptococcosis after kidney transplantation from the graft patterns of kidney injury to the long term outcomes. Method We established a nationwide cohort of adult kidney transplant recipients diagnosed with cryptococcosis between 2002 and 2019 in France. All data were gathered starting from the transplantation date and encompassed up to the latest follow-up consultation. All putative causes of AKI as claimed by the attending clinicians were recorded. Cases were matched (ratio 1:6) with kidney transplant recipients from the French prospective multicenter cohort DIVAT with parameters at time of transplant including immunosuppression and known risk factors of cryptococcosis such as age, history of smoke, history of cancer and HIV status. Transplant outcomes (graft failure and patient death) were then compared between matched patients. Results 88 patients were included. Patients were predominantly male (n = 61, 69.3%), with a mean age of 57.0 years [SD ±13.3]. The majority of patients were primary kidney transplants (n = 71, 80.7%) with a median time from ESRD to transplantation of 2.8 years [IQ 1.25-5]. The majority of patients received ATG as induction therapy for their transplant (n = 50, 69.4%)Acute kidney injury (AKI) at diagnosis involved 37.3% of the patients with 13.3% requiring renal replacement therapy. AKI staging was distributed as follows, AKI grade 1 in 12.5% of patients, grade 2 in 13.3% of patients, and grade 3 in 11.5% of patients. During the induction stage, 39% of patients developed amphotericin B-related AKI. AKI resulting from tacrolimus overdose subsequent to tacrolimus/fluconazole interaction occurred in 25.7% of patients during the consolidation stage. Among the patients alive at 3 months following the diagnosis of cryptococcosis, 33.7% of patients exhibited graft dysfunction. Following cryptococcosis, 5 patients displayed T cell rejection and 4 patients developed antibody-mediated rejection. A total of 41 patients with cryptococcosis were matched to 246 controls (ratio 1:6), after a median follow-up of 52.3 [28.1-90.2] months, patients with cryptococcosis exhibited a higher risk of mortality with 35.9% compared with 9.8% (p < 0.001) and graft failure with 33.3% compared with 15.0% (p = 0.0005). Conclusion This study has shown that kidney injury manifests itself through a sequential, multi-step process that initially includes pre-renal impairment, ATN and iatrogenic mechanisms. Amphotericin B-related AKI, followed by tacrolimus overdose represent common causes of AKI.

DNA Damage and Parkinson's Disease.

The etiology underlying most sporadic Parkinson's' disease (PD) cases is unknown. Environmental exposures have been suggested as putative causes of the disease. In cell models and in animal studies, certain chemicals can destroy dopaminergic neurons. However, the mechanisms of how these chemicals cause the death of neurons is not understood. Several of these agents are mitochondrial toxins that inhibit the mitochondrial complex I of the electron transport chain. Familial PD genes also encode proteins with important functions in mitochondria. Mitochondrial dysfunction of the respiratory chain, in combination with the presence of redox active dopamine molecules in these cells, will lead to the accumulation of reactive oxygen species (ROS) in dopaminergic neurons. Here, I propose a mechanism regarding how ROS may lead to cell killing with a specificity for neurons. One rarely considered hypothesis is that ROS produced by defective mitochondria will lead to the formation of oxidative DNA damage in nuclear DNA. Many genes that encode proteins with neuron-specific functions are extraordinary long, ranging in size from several hundred kilobases to well over a megabase. It is predictable that such long genes will contain large numbers of damaged DNA bases, for example in the form of 8-oxoguanine (8-oxoG), which is a major DNA damage type produced by ROS. These DNA lesions will slow down or stall the progression of RNA polymerase II, which is a term referred to as transcription stress. Furthermore, ROS-induced DNA damage may cause mutations, even in postmitotic cells such as neurons. I propose that the impaired transcription and mutagenesis of long, neuron-specific genes will lead to a loss of neuronal integrity, eventually leading to the death of these cells during a human lifetime.

Identification of shared molecular mechanisms and diagnostic biomarkers between heart failure and idiopathic pulmonary fibrosis

BackgroundHeart failure (HF) and idiopathic pulmonary fibrosis (IPF) are global public health concerns. The relationship between HF and IPF is widely acknowledged. However, the interaction mechanisms between these two diseases remain unclear, and early diagnosis is particularly difficult. Through the integration of bioinformatics and machine learning, our work aims to investigate common gene features, putative molecular causes, and prospective diagnostic indicators of IPF and HF. MethodsThe Gene Expression Omnibus (GEO) database provided the RNA-seq datasets for HF and IPF. Utilizing a weighted gene co-expression network analysis (WGCNA), possible genes linked to HF and IPF were found. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) were then employed to analyze the genes that were shared by HF and IPF. Using the cytoHubba and iRegulon algorithms, a competitive endogenous RNA (ceRNA) network was built based on seven basic diagnostic indicators. Additionally, hub genes were identified using machine learning approaches. External datasets were used to validate the findings. Lastly, the association between the number of immune cells in tissues and the discovered genes was estimated using the CIBERSORT method. ResultsIn total, 63 shared genes were identified between HF- and IPF-related modules using WGCNA. Extracellular matrix (ECM)/structure organization, ECM-receptor interactions, focal, and protein digestion and absorption, were shown to be the most enrichment categories in GO and KEGG enrichment analysis of common genes. Furthermore, a total of seven fundamental genes, including COL1A1, COL3A1, THBS2, CCND1, ASPN, FAP, and S100A12, were recognized as pivotal genes implicated in the shared pathophysiological pathways of HF and IPF, and TCF12 may be the most important regulatory transcription factor. Two characteristic molecules, CCND1 and NAP1L3, were selected as potential diagnostic markers for HF and IPF, respectively, using a support vector machine-recursive feature elimination (SVM-RFE) model. Furthermore, the development of diseases and diagnostic markers may be associated with immune cells at varying degrees. ConclusionsThis study demonstrated that ECM/structure organisation, ECM-receptor interaction, focal adhesion, and protein digestion and absorption, are common pathogeneses of IPF and HF. Additionally, CCND1 and NAP1L3 were identified as potential diagnostic biomarkers for both HF and IPF. The results of our study contribute to the comprehension of the co-pathogenesis of HF and IPF at the genetic level and offer potential biological indicators for the early detection of both conditions.

Genetic insight into putative causes of xanthelasma palpebrarum: a Mendelian randomization study.

Xanthelasma palpebrarum (XP) is the most common form of cutaneous xanthoma, with a prevalence of 1.1%~4.4% in the population. However, the cause of XP remains largely unknown. In the present study, we used Mendelian randomization to assess the genetic association between plasma lipids, metabolic traits, and circulating protein with XP, leveraging summary statistics from large genome-wide association studies (GWAS). Genetically predicted plasma cholesterol and LDL-C, but not HDL-C or triglyceride, were significantly associated with XP. Metabolic traits, including BMI, fasting glucose, type 2 diabetes, systolic and diastolic blood pressure, were not significantly associated with XP. Furthermore, we found genetically predicted 12 circulating proteins were associated with XP, including FN1, NTM, FCN2, GOLM1, ICAM5, PDE5A, C5, CLEC11A, CXCL1, CCL2, CCL11, CCL13. In conclusion, this study identified plasma cholesterol, LDL-C, and 12 circulating proteins to be putative causal factors for XP, highlighting the role of plasma cholesterol and inflammatory response in XP development.

Husbandry conditions of spotted ratfish (Hydrolagus colliei, Chimaeriformes) in aquaria for successful embryonic development and long-term survival of juveniles.

The spotted ratfish Hydrolagus colliei is the most common holocephalan species exhibited in aquaria worldwide for introducing deep-sea environments and raising awareness of their conservation. However, little is known about the biology of H. colliei. Current practices in aquaria allow long-term survival of sexually mature H. colliei specimens; however, this species struggles to complete a reproductive cycle in captivity mostly because embryos do not reach the hatchling stage. The aquarists of Planet Ocean Montpellier (POM, France) have bred H. colliei for 15 years and recorded parameters suitable for this species' successful embryonic and post-embryonic development. POM aquarists now regularly record egg-laying events of H. colliei and use four tanks to incubate eggs and raise neonates, late hatchlings, early and intermediate juveniles, subadults, and sexually mature specimens. In this work we provide the first long-term biometric data on H. colliei from the hatchling to the subadult stage. We also report the biotic and abiotic parameters sufficient to breed H. colliei in aquaria. We finally describe the methods used to facilitate individual monitoring of specimens along the ontogeny and several pathologies identified in this species, their putative causes, and the corresponding treatments. This work highlights the importance of ex situ research and points to the valuable outcomes of collaborative efforts between aquaria and academia in deciphering the biology of species whose study in the wild remains challenging.

In vitro dose-dependent effects of matrix metalloproteinases on ECM hydrogel biodegradation

Matrix metalloproteinases (MMPs) cause proteolysis of extracellular matrix (ECM) in tissues affected by stroke. However, little is known about how MMPs degrade ECM hydrogels implanted into stroke cavities to regenerate lost tissue. To establish a structure-function relationship between different doses of individual MMPs and isolate their effects in a controlled setting, an in vitro degradation assay quantified retained urinary bladder matrix (UBM) hydrogel mass as a measure of degradation across time. A rheological characterization indicated that lower ECM concentrations (<4 mg/mL) did not cure completely at 37 °C and had a high fraction of mobile proteins that were easily washed-out. Hydrolysis by dH2O caused a steady 2 % daily decrease in hydrogel mass over 14 days. An acceleration of degradation to 6 % occurred with phosphate buffered saline and artificial cerebrospinal fluid. MMPs induced a dose-dependent increase and within 14 days almost completely (>95 %) degraded the hydrogel. MMP-9 exerted the most significant biodegradation, compared to MMP-3 and -2. To model the in vivo exposure of hydrogel to MMPs, mixtures of MMP-2, -3, and -9, present in the cavity at 14-, 28-, or 90-days post-stroke, revealed that 14- and 28-days mixtures achieved an equivalent biodegradation, but a 90-days mixture exhibited a slower degradation. These results revealed that hydrolysis, in addition to proteolysis, exerts a major influence on the degradation of hydrogels. Understanding the mechanisms of ECM hydrogel biodegradation is essential to determine the therapeutic window for bioscaffold implantation after a stroke, and they are also key to determine optimal degradation kinetics to support tissue regeneration. Statement of significanceAfter implantation into a stroke cavity, extracellular matrix (ECM) hydrogel promotes tissue regeneration through the degradation of the bioscaffold. However, the process of degradation of an ECM hydrogel remains poorly understood. We here demonstrated in vitro under highly controlled conditions that hydrogel degradation is very dependent on its protein concentration. Lower protein concentration hydrogels were weaker in rheological measurements and particularly susceptible to hydrolysis. The proteolytic degradation of tissue ECM after a stroke is caused by matrix metalloproteinases (MMPs). A dose-dependent MMP-driven biodegradation of ECM hydrogel exceeded the effects of hydrolysis. These results highlight the importance of in vitro testing of putative causes of degradation to gain a better understanding of how these factors affect in vivo biodegradation.

How deep is the cut? The influence of daily microaggressions on bisexual women's health.

Bisexual women experience disproportionately poorer health outcomes in comparison to lesbian and gay groups, and the general population, including inequities related to mental and physical health. Although bisexual-specific health inequities are increasingly well-documented, research examining putative causes of such inequities, as well as research that accounts for differences within bisexual populations - particularly among racial minorities- remains limited. To address these gaps, this paper reports findings from the Women's Daily Experiences Study (WoDES), a multi-method study that explored the relationship between microaggressions and health outcomes among racially/ethnically diverse cisgender, bisexual women in Chicago. Data from 28-day daily e-diaries (N = 2,104 observations; 99 participants, 57% women of color) were analyzed using multilevel modeling to (1) measure the frequency of microaggressions among bisexual women; (2) examine the influence of sexual orientation, racial, and gender microaggressions on mental and physical health; and (3) investigate how race influences relationships between microaggressions and health. Participants reported an average of 8.1 microaggressions in the previous 28 days, and at least one microaggression was reported for more than 42% of days (n = 802). Microaggressions of any type were associated with increased same-day negative affect and somatic complaints. Latina bisexual women experienced worse health outcomes in comparison to Black bisexual women. This study demonstrated the detrimental impact of microaggressions on the health of bisexual women and highlights the critical need for strategies on broader structural changes that could improve the health and well-being of bisexual women.

Assessment of Clinical, Histopathological, and Bacteriological Findings in Treated Leprosy Patients with Persistent Skin Lesions: A Retrospective Cohort Study.

Since the introduction of multidrug therapy (MDT), various disabilities/morbidities due to leprosy have been prevented. However, there is a subset of patients in whom the skin lesions do not resolve completely or remain unchanged despite a full course of MDT, which is a great source of anxiety to the patient and their family members. Hence, we tried to ascertain the putative causes and risk factors of persistent skin lesions (PSLs) by analyzing the clinical, histopathological, bacteriological, and drug resistance patterns. This is a retrospective, cohort study wherein 35 patients who had PSLs after completion of MDT were included. The majority of the patients were 18 to 30 years of age, with males predominating. Borderline tuberculoid leprosy was the most common clinical spectrum observed (71.4%). The majority had PSLs distributed predominantly over photo-exposed sites (upper limbs > trunk > face). Eight patients (22.8%) had a history of contact with leprosy patients in their family, and six patients (17.1%) had associated comorbidities. Improvement in histopathological parameters such as a decrease in granuloma fraction was observed in 22 patients (62.8%) with PSLs after release from treatment in comparison with baseline. Four patients (11.4%) were noted to have drug resistance (three to rifampicin and one to dapsone). Thus, our study emphasizes that leprosy patients with PSLs after completion of MDT should undergo histopathological evaluation and drug resistance studies.

The paradox of predation studies.

Understanding the causal relationships that contribute to mortality in populations is a priority for epidemiology, animal husbandry and ecology. Of all the sources of mortality in nature, predation is perhaps the most important, while simultaneously being one of the most difficult to study and understand. In this opinion piece, we use the epidemiological concept of the sufficient-component cause model to outline why we believe that predation studies often misrepresent predators as sufficient cause of death (or natural mortality) in ecological studies. This is pivotal in conservation biology because such studies have often led to demands for predator removal throughout the world. We use the sufficient-component cause model to illustrate the paradox that multiple studies, each studying singular putative causes of mortality (including predation), will sum to more than 100% mortality when added together. We suggest that the sufficient-component framework should be integrated into both fundamental and applied ecology to better understand the role of predators in natural ecosystems.

The spread of satellite DNAs in euchromatin and insights into the multiple sex chromosome evolution in Hemiptera revealed by repeatome analysis of the bug Oxycarenus hyalinipennis.

Satellite DNAs (satDNAs) are highly repeated tandem sequences primarily located in heterochromatin, although their occurrence in euchromatin has been reported. Here, our aim was to advance the understanding of satDNA and multiple sex chromosome evolution in heteropterans. We combined cytogenetic and genomic approaches to study, for the first time, the satDNA composition of the genome in an Oxycarenidae bug, Oxycarenus hyalinipennis. The species exhibits a male karyotype of 2n = 19 (14A + 2 m + X1 X2 Y), with a highly differentiated Y chromosome, as demonstrated by C-banding and comparative genomic hybridization, revealing an enrichment of repeats from the male genome. Additionally, comparative analysis between males and females revealed that the 26 identified satDNA families are significantly biased towards male genome, accumulating in discrete regions in the Y chromosome. Exceptionally, the OhyaSat04-125 family was found to be distributed virtually throughout the entire extension of the Y chromosome. This suggests an important role of satDNA in Y chromosome differentiation, in comparison of other repeats, which collectively shows similar abundance between sexes, about 50%. Furthermore, chromosomal mapping of all satDNA families revealed an unexpected high spread in euchromatic regions, covering the entire extension, irrespective of their abundance. Only discrete regions of heterochromatin on the Y chromosome and of the m-chromosomes (peculiar chromosomes commonly observed in heteropterans) were enriched with satDNAs. The putative causes of the intense enrichment of satDNAs in euchromatin are discussed, including the possible existence of burst cycles similar to transposable elements and as a result of holocentricity. These data challenge the classical notion that euchromatin is not enriched with satDNAs.

From Association to Intervention: The Alzheimer's Disease-Associated Processes and Targets (ADAPT) Ontology.

Many putative causes and risk factors have been associated with outcomes in Alzheimer's disease (AD) but all attempts at disease-modifying treatment have failed to be clinically significant. Efforts to address this "association-intervention" mismatch have tended to focus on the novel design of interventions. Here, we instead deal with the notion of association in depth. We introduce the concept of disease-associated process (DAP) as a flexible concept that can unite different areas of study of AD from genetics to epidemiology to identify disease-modifying targets. We sort DAPs using three properties: specificity for AD, frequency in patients, and pathogenic intensity for dementia before using a literature review to apply these properties in three ways. Firstly, we describe and visualize known DAPs. Secondly, we exemplify qualitative specificity analysis with the DAPs of tau protein pathology and autophagy to reveal their differential implication in AD. Finally, we use DAP properties to define the terms "risk factor," "cause," and "biomarker." We show how DAPs fit into our collaborative disease ontology, the Alzheimer's Disease-Associated Processes and Targets (ADAPT) ontology. We argue that our theoretical system can serve as a democratic research forum, offering a more biologically adequate view of dementia than reductionist models. The ADAPT ontology is a tool that could help to ground debates around priority setting using objective criteria for the identifying of targets in AD. Further efforts are needed to address issues of how biomedical research into AD is prioritized and funded.

A 91% decline in a common anuran in an otherwise stable amphibian community inferred from 17 years of rapid road surveys

AbstractAmphibians are disproportionately represented among the many vertebrate taxa that are declining globally. Few long‐term studies of amphibians exist, especially in temperate climates, hindering our understanding of long‐term trends in amphibian communities, which may delay or prevent management action. Here, we develop and deploy an inexpensive monitoring method with potentially broad scientific and community uptake, ‘rapid road surveys’. We test whether this protocol is useful in understanding relative abundance in an amphibian community over a 17‐year period. From 2003 to 2019, we performed thousands of rapid (5–15 min) amphibian surveys and recorded the number of on‐road amphibians along a single, 267 m stretch of secondary roads in rural Canada. Assuming that on‐road occurrence reflects relative amphibian population sizes, we show that amphibians have declined by approximately 73% from 2003 to 2019. The decline was driven by a remarkable 91% decrease in the abundance of northern leopard frogs (Lithobates pipiens), the species comprising the most observation records, while all other species did not show a temporal trend. We cannot attribute a definitive mechanism to the L. pipiens decline. However, by ruling out a number of putative causes, we hypothesize that it may be related to land‐use change or infectious disease. Our results show that a simple, temporally replicated road survey protocol, deployed in a spatially restricted area, can be a valuable tool for conservation scientists to understand trends in abundance across an entire community. We discuss how these rapid road surveys are likely a viable option for future community science initiatives.

Evaluating the Impact of Commonly Used Pesticides on Honeybees (Apis mellifera) in North Gonder of Amhara Region, Ethiopia.

Global honeybee losses and colony decline are becoming continuous threat to the apicultural industry, as well as, for food security and environmental stability. Although the putative causes are still unclear, extensive exposure of bees to pesticides could be the possible factor for worldwide colony losses. This study was aimed at evaluating the impact of nine commonly used pesticide incidents on adult worker honeybees (A. mellifera) under the laboratory condition, in North Gonder of Amhara region, Ethiopia. Feeding test, contact test, and fumigation tests were carried out for each pesticide following the standard procedures, and each pesticide toxicity was compared to the standard toxic chemical, dimethoate 40% EC (positive control), and to 50% honey solution (negative control). The results revealed that all the tested pesticides caused significant deaths of the experimental bees (P < 0.05) in all the tests when compared to the negative control. Diazinon 60% EC, endosulfan 35% EC, and malathion 50% EC were appeared highly toxic causing 100% mortality of bees, while chlorsulfuron 75% WG killed 90% of the experimental bees as tested via feeding. On the other hand, agro-2, 4-D and its mixture with glycel 41% EC are moderately toxic, and mancozeb 80% WP and glycel 41% EC were slightly toxic to honeybees as compared to the positive control (dimethoate 40% EC). Suddenly, diazinon 60% EC and malathion 50% EC triggered 100% mortality of bees, while endosulfan 35% EC and chlorsulfuron 75% WG caused 63.63% and 90.82% of bee mortality, respectively, when evaluated via contact test. The fumigation test also showed that chlorsulfuron 75% WG, diazinon 60% EC, and endosulfan 35% EC caused 100%, 86.7%, and 65.6% mortality rate of bees. Our result also highlighted that tested LD50 of all pesticide incidents were significantly lower than the manufacturer-based LD50. This shows that local honeybees A. m. jemenetica are extremely sensitive to commonly used agricultural pesticides, which may affect the colony level due to the intensive application of these pesticides in Ethiopia.

Missing in action: Reference sites

White et al. (2023) measured land area with precision in coastal areas exposed to river diversions, but the absence of concurrent measurements in reference sites prohibits them from making conclusions, which they do, that river diversions have a beneficial or neutral consequences but not harmful effects. Their global conclusions about land gain are inappropriate for analyses of areas embedded in ecosystems when there are no reference areas included in the analysis. Their inferences about the temporal on-site changes are valid, but measurements in suitable reference sites are needed to separate out the environmental ‘noise’ common to both and to allow conclusions about putative causes. Environmental impacts are typically discerned within a Before-After-Control-Impact (BACI) analysis. White et al.'s study design is a’BA’, but not a BACI design. They are critical of one of two of Turner et al.'s (2019) photogrammetric methods, but neglect to realize that the different methods reveal different aspects of land loss and are used independently of each other within a BACI framework having multiple reference sites. They also neglect to account for 1) results from a BACI analysis of thirty-two sites from farther downstream, 2) a striking loss of land after a natural river diversion opened up in 1973, and 3) they omit important information placing sediment retention into context. The problem of omitting reference sites in evaluations of environmental impacts is commonly observed and deserves wider attention to improve the general ecological intelligence of responsible parties and lay communities. Treating environmental projects a priori as experiments with testable hypotheses with alternative outcomes and actionable exit strategies will reduce errors and bias in endeavors with many unexpected unknowns.

Mapping myelin in white matter with T1-weighted/T2-weighted maps: discrepancy with histology and other myelin MRI measures

The ratio of T1-weighted/T2-weighted magnetic resonance images (T1w/T2w MRI) has been successfully applied at the cortical level since 2011 and is now one of the most used myelin mapping methods. However, no reports have explored the histological validity of T1w/T2w myelin mapping in white matter. Here we compare T1w/T2w with ex vivo postmortem histology and in vivo MRI methods, namely quantitative susceptibility mapping (QSM) and multi-echo T2 myelin water fraction (MWF) mapping techniques. We report a discrepancy between T1w/T2w myelin maps of the human corpus callosum and the histology and analyse the putative causes behind such discrepancy. T1w/T2w does not positively correlate with Luxol Fast Blue (LFB)-Optical Density but shows a weak to moderate, yet significant, negative correlation. On the contrary, MWF is strongly and positively correlated with LFB, whereas T1w/T2w and MWF maps are weakly negatively correlated. The discrepancy between T1w/T2w MRI maps, MWF and histological myelin maps suggests caution in using T1w/T2w as a white matter mapping method at the callosal level. While T1w/T2w imaging may correlate with myelin content at the cortical level, it is not a specific method to map myelin density in white matter.