Local Patterns Research Articles

Local adaptation can cause both peaks and troughs in nucleotide diversity within populations.

The amount of standing variation present within populations is a fundamental quantity of interest in population genetics, commonly represented by calculating the average number of differences between pairs of nucleotide sequences (nucleotide diversity, π). It is well understood that both background and positive selection can cause reductions in nucleotide diversity, but less clear how local adaptation affects it. Depending on the assumptions and parameters, some theoretical studies have emphasized how local adaptation can reduce nucleotide diversity, while others have shown that it can increase it. Here, we explore how local adaptation shapes genome-wide patterns in within-population nucleotide diversity, extending previous work to study the effects of polygenic adaptation, genotypic redundancy, and population structure. We show that local adaptation produces two very different patterns depending on the relative strengths of migration and selection, either markedly decreasing or increasing within-population diversity at linked sites at equilibrium. At low migration, regions of depleted diversity can extend large distances from the causal locus, with substantially more diversity eroded than expected with background selection. With higher migration, peaks occur over much smaller genomic distances but with much larger magnitude changes in diversity. Across spatially extended environmental gradients, both patterns can be found within a single species, with increases in diversity at the center of the range and decreases towards the periphery. Our results demonstrate that there is no universal diagnostic signature of local adaptation based on within-population nucleotide diversity, so it will not be broadly useful for explaining increased FST. However, given that neither background nor positive selection inflate diversity, when peaks are found they suggest local adaptation may be acting on a causal allele in the region.

Prevalence and resistance of Helicobacter pylori in a predominantly Hispanic population.

Helicobacter pylori (H. pylori) is the most common chronic bacterial infection in humans. The risk of acquiring H. pylori is related to socioeconomic status and living conditions early in life. Treatment regimens must consider local antibiotic resistance patterns. Adventist Health White Memorial Hospital serves a predominantly indigent population in east Los Angeles with a large number of immigrants from South and Central America. Data regarding the prevalence and resistance of H. pylori in this population is scant. To evaluate the prevalence and resistance of H. pylori and correlate with country of origin. All gastric biopsies were obtained by a single gastroenterologist at the hospital in a consecutive manner from patients with gastritis from 2017 to 2022 and sent to various labs for evaluation. Two hundred and sixty-six patients are born in the United States, 450, 171, 70, and 30 patients are immigrants from Mexico, Central and South America (CSA), Asia, and other countries respectively. Overall, 14.65% were found to be infected with H. pylori. Rates of infection in United States-born citizens, immigrants from Mexico, CSA, and Asia are 9.02%, 18.67%, 13.45%, and 11.43% respectively, with Mexican immigrants having a relative risk of 2.3889 [95% confidence interval (CI): 1.4789-3.8588, P = 0.0004] compared to those born in United States. No correlation seen between infection and length of time immigrants were in United States. Relative risk of infection in patients with no proton pump inhibitor use within the past 30 days found to be 1.9276 (95%CI: 1.3562-2.7398, P = 0.0003). Rates of resistance for clarithromycin and levofloxacin are 21.43% and 31.11%. H. pylori infection appears to be associated with low socioeconomic status and poor living conditions early in life. Clarithromycin and levofloxacin based treatment regimens should be avoided as first line therapy in this region, particularly in patients of Latin American origin.

The Pangolin Universal Notching System: a scale-marking methodology for pangolins

Abstract Despite thousands of individuals entering the illegal wildlife trade each year, assessments of pangolin populations are largely non-existent, even in areas with high exploitation and limited personnel and field equipment. Although pangolins have unique keratin-based scales, there is no universal scale-marking method for individuals despite some pangolin conservation programmes utilizing marking for reference and cataloguing. Each programme currently establishes and manages its own system, resulting in inconsistencies and limiting data sharing. To facilitate pangolin monitoring and research, we developed a standardized method for assigning individual identification numbers, which we call the Pangolin Universal Notching System. This system is neither resource nor training intensive, which could facilitate its adoption and implementation globally. Its application could help to address knowledge gaps in pangolin ageing, reproduction, survivorship, migration and local trafficking patterns, and could be used in combination with other tagging techniques for research on pangolin biology.

Alzheimer’s disease (AD) classification using MRI: A deep ensemble model with modified local pattern feature set

The Alzheimer disease (AD) is a neurologic brain condition, which affects the cells in the brain and eventually renders a patient incapable of performing routine daily tasks. Due to the outstanding spatial clarity, high access, and strong contrast, MRI has been utilized in analyses pertaining to AD. This work develops an AD classification model using MRI images. Here, preprocessing is done by the Gabor filter. Subsequently, the Improved U-net segmentation model is employed for image segmentation. The features extracted comprises of modified LGXP features, LTP features, and LBP features as well. Finally, the Deep ensemble classifier (DEC) model is proposed for AD classification which combines classifiers such as RNN, DBN, and Deep Maxout Network (DMN). For enhancing the efficiency for classification of AD, the optimal weight of DMN is adjusted using the Self Customized BWO (SC-BWO) model. The outputs from DEC are averaged and the final result is obtained. Finally, the analysis of dice, Jaccard scores is performed to show the betterment of the SC-BWO scheme.

Local Invasion Patterns Characterized by SARIFA and Tumor Budding Differ and Have Distinct Prognostic Significance in Esophageal Adenocarcinoma and Squamous Cell Carcinoma.

Both esophageal squamous cell carcinoma (ESQCC) and adenocarcinoma (EAC) are known to have poor prognosis. We aimed to investigate the invasion front areas of 57 ESQCC and 43 EAC cases to find histological signs of metastatic progression. Tumor cell clusters with different cell counts, including tumor buds (TBs) and poorly differentiated clusters (PDCs), were assessed. The presence of the recently described Stroma AReactive Invasion Front Area (SARIFA) phenomenon, which defines a direct contact between tumor cells and adipocytes, was more frequently observed in EAC than in ESQCC (p = 0.004). In adenocarcinomas, a higher prevalence of SARIFA was observed in tumors with a higher number of small clusters (TBs and small PDCs; p < 0.001); furthermore, both the high number of TBs (p = 0.016) and the presence of SARIFA (p = 0.001) correlated with a higher pT stage. SARIFA positivity in EAC (p = 0.011) and high TB in ESQCC (p = 0.0006) were found to be independent prognostic factors for lymph node metastases. Moreover, in ESQCC, the higher absolute number of both TBs and PDCs was associated with shorter overall survival (p = 0.0269 and p = 0.0377, respectively). Our results suggest that the histological subtypes of esophageal cancer behave differently, namely, that different features of the invasion front are of prognostic significance.

Physiological resilience of intertidal chitons in a persistent upwelling coastal region

Current climate projections for mid-latitude regions globally indicate an intensification of wind-driven coastal upwelling due to warming conditions. The dynamics of mid-latitude coastal upwelling are marked by environmental variability across temporal scales, which affect key physiological processes in marine calcifying organisms and can impact their large-scale distribution patterns. In this context, marine invertebrates often exhibit phenotypic plasticity, enabling them to adapt to environmental change. In this study, we examined the physiological performance (i.e., metabolism, Thermal Performance Curves, and biomass and calcification rates) of individuals of the intertidal mollusk Chiton granosus, a chiton found from northern Peru to Cape Horn (5° to 55°S). Our spatial study design indicated a pattern of contrasting conditions among locations. The Talcaruca site, characterized by persistent upwelling and serving as a biogeographic break, exhibited lower pH and carbonate saturation states, along with higher pCO2, compared to the sites located to the north and south of this location (Huasco and Los Molles, respectively). In agreement with the spatial pattern in carbonate system parameters, long-term temperature records showed lower temperatures that changed faster over synoptic scales (1–15 days) at Talcaruca, in contrast to the more stable conditions at the sites outside the break. Physiological performance traits from individuals from the Talcaruca population exhibited higher values and more significant variability, along with significantly broader and greater warming tolerance than chitons from the Huasco and Los Molles populations. Moreover, marked changes in local abundance patterns over three years suggested population-level responses to the challenging environmental conditions at the biogeographic break. Thus, C. granosus from the Talcaruca upwelling zone represents a local population with wide tolerance ranges that may be capable of withstanding future upwelling intensification on the Southern Eastern Pacific coast and likely serving as a source of propagules for less adapted populations.

3D Shape Completion on Unseen Categories: A Weakly-Supervised Approach.

3D shapes captured by scanning devices are often incomplete due to occlusion. 3D shape completion methods have been explored to tackle this limitation. However, most of these methods are only trained and tested on a subset of categories, resulting in poor generalization to unseen categories. In this paper, we propose a novel weakly-supervised framework to reconstruct the complete shapes from unseen categories. We first propose an end-to-end prior-assisted shape learning network that leverages data from the seen categories to infer a coarse shape. Specifically, we construct a prior bank consisting of representative shapes from the seen categories. Then, we design a multi-scale pattern correlation module for learning the complete shape of the input by analyzing the correlation between local patterns within the input and the priors at various scales. In addition, we propose a self-supervised shape refinement model to further refine the coarse shape. Considering the shape variability of 3D objects across categories, we construct a category-specific prior bank to facilitate shape refinement. Then, we devise a voxel-based partial matching loss and leverage the partial scans to drive the refinement process. Extensive experimental results show that our approach is superior to state-of-the-art methods by a large margin. We will make the source code publicly available at https://github.com/ltwu6/WSSC.

Antimicrobial Drug Utilization and Resistance Trends in Septicemia Patients: A Comprehensive Study at a Tertiary Care Hospital

Background: Septicemia is still among the leading causes of morbidity and mortality worldwide, especially among patients in the intensive care unit. The right use of antimicrobial agents is central to the successful management of septicemia, but increasing incidences of antimicrobial resistance are a big challenge. Objective: This study aimed to quantify the antimicrobial usage, resistant organisms, and clinical performance in septicemia patients in a tertiary healthcare facility in Bangladesh. Methods: A prospective observational study was done in the Department of Medicine, Community Based Medical College Hospital, over a period of 16 months. One hundred and ten participants with septicemia and admitted to the ICU were recruited. Demographic data, antimicrobial consumption, microbiological results, and clinical outcomes were gathered and examined. Results: Most of the patients were male (54.5%) and within the age group of 31–40 years. Cephalosporins were the most common first-line antimicrobials (13.3%), while macrolides (12.3%) and carbapenems (11.7%) were at the second and third rank, respectively. There were frequent alterations in antimicrobial therapy; in 28 percent of cases, ceftriaxone was replaced by levofloxacin. Patients with resistant infections had the advantage of a longer hospital and ICU stay of at least 1 week (p&lt;0.01). 16% in patients with resistant infections. Conclusion: The topics discussed in this study include the issues arising from septicemia management due to antimicrobial resistance, the requirement of broad-spectrum empiric therapy, often changing antimicrobial regimens, and overall poor outcomes for such resistant infections. Overall, the present results highlight the need for strict adherence to principles of antimicrobial stewardship, local resistance pattern monitoring, and the creation of novel therapeutic interventions. Additional multi-centered trials to determine strategies against septicemia and AMR in limited resource .........

Mortality risk predicts global, local, and individual patterns of human reproduction

BackgroundHuman reproductive dynamics in the post-industrial world are typically explained by economic, technological, and social factors including the prevalence of contraception and increasing numbers of women in higher education and the workforce. These factors have been targeted by multiple world governments as part of family policies, yet those policies have had limited success. The current work adopts a life history perspective from evolutionary biology: like most species, human populations may respond to safer environments marked by lower morbidity and mortality by slowing their reproduction and reducing their number of offspring. We test this association on three levels of analysis using global, local, and individual data from publicly available databases.ResultsData from over 200 world nations, 3,000 U.S. counties and 2,800 individuals confirm an association between human reproductive outcomes and local mortality risk. Lower local mortality risk predicts “slower” reproduction in humans (lower adolescent fertility, lower total fertility rates, later age of childbearing) on all levels of analyses, even while controlling for socioeconomic variables (female employment, education, contraception).ConclusionsThe association between extrinsic mortality risk and reproductive outcomes, suggested by life history theory and previously supported by both animal and human data, is now supported by novel evidence in humans. Social and health policies governing human reproduction, whether they seek to boost or constrain fertility, may benefit from incorporating a focus on mortality risk.

双行轮式自走型大白菜收获机设计与试验

Aiming at the problems of low harvesting level of Chinese cabbage, high cost of manual operation and lack of special harvesting machinery, a double-row wheeled self-propelled Chinese cabbage harvester was designed on the basis of measuring the physical parameters of 'Zaofeng 01'Chinese cabbage varieties and combining with the main local planting patterns. It can complete the root cutting, pulling, clamping and conveying, packing and collecting of double-row Chinese cabbage at one time. Through the design and selection of the key working parts of the double-row wheel self-propelled Chinese cabbage harvester prototype, the key working parameters of the profiling device, the root cutting-pulling device and the clamping conveying device were determined. The kinematics analysis of the harvester in the profiling, cutting, pulling, clamping and conveying links was carried out, and the field operation performance test of the prototype was completed. The results showed that: when the rotation speed of the cutter was 280 r/min, the rotation speed of the clamping conveyor belt was 240 r/min, and the forward speed of the machine was 1.44 km/h, the maximum qualified rate of harvesting was 95.08 %, the minimum value was 90.65 %, and the average value was 93.79 %. At this time, the working performance of the working machine is stable, the harvesting effect is good, and all performance indicators meet the relevant design requirements and standards. The research results can provide reference for the development and structural improvement of Chinese cabbage low-loss harvesting equipment.

Volunteers Track Parisian Pollution with the Help of Tree Bark

Participants in the Ecorc’Air project are using magnetic particles deposited on tree bark to reveal local traffic pollution patterns.

Aerial-view geo-localization based on multi-layer local pattern cross-attention network

Aerial-view geo-localization based on multi-layer local pattern cross-attention network

Enhancing emotion detection with synergistic combination of word embeddings and convolutional neural networks

Recognizing emotions in textual data is crucial in a wide range of natural language processing (NLP) applications, from consumer sentiment research to mental health evaluation. The word embedding techniques play a pivotal role in text processing. In this paper, the performance of several well-known word embedding methods is evaluated in the context of emotion recognition. The classification of emotions is further enhanced using a convolutional neural network (CNN) model because of its propensity to capture local patterns and its recent triumphs in text-related tasks. The integration of CNN with word embedding techniques introduced an additional layer to the landscape of emotion detection from text. The synergy between word embedding techniques and CNN harnesses the strengths of both approaches. CNNs extract local patterns and features from sequential data, making them well-suited for capturing relevant information within the embeddings. The results obtained with various embeddings highlight the significance of choosing synergistic combinations for optimum performance. The combination of CNNs and word embeddings proved a versatile and effective approach.

The JA-to-ABA signaling relay promotes lignin deposition for wound healing in Arabidopsis

Plants are frequently exposed to herbivory and mechanical damage that result in wounding. Two fundamental strategies, regeneration and healing, are employed by plants upon wounding. How plants make different decisions and how wound healing is sustained until the damaged tissues recover are not fully understood. In this study, we found that local auxin accumulation patterns, determined by wounding modes, may activate different recovery programs in wounded tissues. Wounding triggers transient jasmonic acid (JA) signaling that promotes lignin deposition in the first few hours after wounding occurs. This early response is subsequently relayed to ABA signaling via MYC2. The induced JA signaling promotes ABA biosynthesis to maintain the expression of RAP2.6, a key factor for sustained lignin biosynthesis and the later wound-healing process. Our findings provide mechanistic insights into how plants heal from wounding and clarify the molecular mechanisms that underlie the prolonged healing process following wounding.

Numerical investigation of heat transfer characteristics of hydrogen flow in a randomly packed bed

In this study, two randomly packed beds with small tube-to-particle diameter (D/d) ratios of D/d = 4 (PB-4) and D/d = 5 (PB-5) are constructed using the discrete element method (DEM). The pore-scale heat transfer characteristics of hydrogen flow at low pore Reynolds numbers (Rep < 100) are investigated using a DEM-CFD simulation approach, with the temperature-dependent thermo-properties of hydrogen being considered. Distinct local channeling flow patterns are revealed by detailed analyses of the flow fields in PB-4 and PB-5. The overall friction factors for both beds are found to agree well with empirical correlations. Notably, a faster spatial temperature increase is exhibited by PB-5, with a larger D/d ratio, as evidenced by a shorter axial distance for fully-heated hydrogen flow compared to PB-4. For the pore-scale heat transfer in the packed beds, the radial temperature profiles are compared at various heights of the packed beds depending on the radial porosity oscillation, in which the wall effect should be especially considered in the near-wall region. Furthermore, the axial pore-scale Nusselt number (Nup,axial) exhibits an inverse fluctuation with the axial porosity oscillation. Finally, the global Nusselt numbers (Nu) in the packed beds are analyzed under different operating conditions, which are in good agreement with empirical correlations.

Microbial keratitis at a single tertiary eye care in Andhra Pradesh: A 12-year analysis of microbiological profile and in vitro susceptibility of bacterial isolates

Abstract: CONTEXT: Microbial keratitis is a potentially vision-threatening emergency that demands prompt diagnosis and treatment to ensure better vision recovery. Empirical use of broad-spectrum antimicrobial therapies is often the primary treatment modality, which is then tailored according to clinical response, cultured organisms, and their sensitivities. Since the spectrum of microbial agents associated with corneal ulcers is wide and varies from one geographical location to another, it is imperative that local microbial trends and susceptibility patterns are analyzed to enable better care in the management of these patients. AIMS: The aim of the study was to report the microbiological profile and in vitro drug susceptibility patterns of bacterial isolates obtained from patients with microbial keratitis in a single tertiary center in Andhra Pradesh over 12 years. METHODS: Microbiology records of culture-positive microbial keratitis that underwent a diagnostic corneal scraping and cultures from the years 2010 to 2021 were reviewed. Trends in bacterial and fungal etiology along with the antibiotic susceptibility profile of bacteria were analyzed. STATISTICAL ANALYSIS USED: Frequency distribution was obtained, and percentages were calculated. RESULTS: Of the 8529 microbial keratitis samples, 3581 corneal scrapings were culture positive which included Gram-positive bacteria (1054/3581, 29.4%), Gram-negative bacteria (476/3581, 13.2%), fungi (2051/3581, 57.2%), and parasites (369/3581, 10.3%). The most common fungal isolate was Fusarium species (557/1748, 31.8%) followed by Aspergillus flavus (495/1748, 28.3%). Similarly, the most common Gram-positive bacteria included Streptococcus pneumoniae (297/891, 33.3%) and Staphylococcus species (213/891, 23.9%), and the most common Gram-negative bacteria was Pseudomonas aeruginosa (294/403, 72.9%). Overall susceptibility patterns showed that Gram-positive bacteria were susceptible to vancomycin (92%), cefazolin (88%), and chloramphenicol (86%), while Gram-negative bacteria were most susceptible to gentamicin and amikacin (81%). The susceptibility to amikacin and gentamicin increased significantly from 71% in 2010 to 92% in 2021 and 74% in 2010 to 92% in 2021, respectively. In comparison, the susceptibility of fluoroquinolones for both Gram-positive and Gram-negative bacteria did not show any significant change over the study period. CONCLUSIONS: The prevalence of fungal and bacterial keratitis has remained unchanged over the years. This study reinforced that fluoroquinolones and vancomycin continue to be good empiric therapies for treating bacterial keratitis in Andhra Pradesh.

Uncovering the multiplex network of global container shipping: Insights from shipping companies

Shipping companies are key drivers of maritime trade and crucial in the development of container shipping networks. Each company's strategy shapes differences in port services and shipping routes, creating a complex and interconnected global container shipping network that is difficult to analyze using single-layer or aggregated models. This paper introduces a novel multiplex network modeling approach that leverages a very large set of AIS data and applies a series of structural indices to reveal the unique characteristics and multiple key roles of various shipping company networks. By applying methods such as overlap ratio analysis, HITS analysis, and community detection, the study identifies differences in overlap between ports and routes, hub and authority properties of individual ports, as well as local and regional patterns within the global network. Furthermore, it examines structural differences between the multiplex network, the aggregated network, and individual layers, highlighting the importance of multiplex container networks in understanding ports' roles on both regional and global scales. The findings clarify how different shipping companies shape shipping network patterns, enhance the multiplex network's functional roles, and provide a better understanding of the complex structure of the Global Container Shipping Network (GCSN). Finally, it provides authorities with valuable insights on how to better understand maritime shipping networks.

The Appropriateness of Empirical Uses of Antibiotics Based on Antimicrobial Susceptibility Results for Inpatients at a Tertiary Hospital in Saudi Arabia.

The optimal use of antibiotics represents a cornerstone in controlling antibiotic resistance. Strategies such as antibiotic stewardship programs (ASPs) have been developed to influence the rational use of antibiotics. This study evaluated the appropriateness of the empirical use of antibiotics based on antibiotic susceptibility results with the aim of participating effectively in improving local ASPs. In a cross-sectional study conducted at a tertiary hospital in Saudi Arabia, 500 inpatients received empirical antibiotics, and their culture and sensitivity results were included. The appropriateness of the empirical use of antibiotics was determined based on their alignment with the culture and sensitivity results. More than half of the participants (56.4%) were men, and nearly half (43%) were over 61 years old. The empirical uses of antibiotics were appropriately prescribed in 58% of the patients. Ciprofloxacin and ceftriaxone were the most prescribed antibiotics, while vancomycin, piperacillin-tazobactam, and tigecycline were the most appropriately prescribed antibiotics. E. coli was the main microorganism isolated in the susceptibility results and was appropriately prescribed in 59% of the patients. The highest microbial sensitivity was observed for linezolid, vancomycin, and tigecycline. Antibiotics were appropriately prescribed empirically in more than half of the participants. Activating interventional ASP is crucial to fill the gap in prescribing antimicrobials. Considering the expected type of organisms and the local susceptibility pattern is likely to yield a more appropriate empirical use of antibiotics.

1739: Local control patterns of GORTEC 2014-04 IIR Trial of SABR or chemo-SABR in oligometastastic HNSCCs

1739: Local control patterns of GORTEC 2014-04 IIR Trial of SABR or chemo-SABR in oligometastastic HNSCCs

Architectural traditions in the structures built by cooperative weaver birds.

Humans cooperate to build complex structures with culture-specific architectural styles. However, they are not the only animals to build complex structures nor to have culture. We show that social groups of white-browed sparrow weavers (Plocepasser mahali) build structures (nests for breeding and multiple single-occupant roosts for sleeping) that differ architecturally among groups. Morphological differences are consistent across years and are clear even among groups with territories a few meters apart. These repeatable differences are not explained by among-group variation in local weather conditions, bird size, tree height, or patterns of genetic relatedness. Architectural styles are also robust to the immigration of birds from other groups.