Philosophical Transactions Research Articles

IMPROVING THE PEER REVIEW PROCESS IN DEVELOPING COUNTRIES

SUMMARY: The peer review process has been regarded as an essential part of accepting or rejecting a paper for publication since 1752 when the process was started by The Royal Society of London in the publication entitled “Philosophical Transactions”. In developing countries, one of the primary reasons for submitting pieces for publication is to support promotion in universities. In fact, the argument can be made that the only reason for publishing in developing countries is for faculty promotion. Despite the peer review process being standard practice for scientic journals, many of the research publications on COVID-19 were not subjected to the peer review system. In fact, numerous publications were pre-prints and papers shared by researchers online which were not peer reviewed, yet they were accepted and published by scientic journals in developing nations. When authors start to lose condence in the peer review process of a journal, they are not likely to submit their research work to such journals and this can lead to a diminished impact and reputation of such journals. Additionally, the selection of the assessors by the Editor-in -Chief is usually from the academic space of the editor and from the colleagues of the editor that usually share the editor's view. Contrary to what some editors in the developing countries believe, medical and academic administrative positions do not necessarily result in expertise in the peer review process. An editor can easily identify a poor assessment of an article, from the vitriolic feed-back of the author to the editor about an assessor when a paper is not recommended for publication. This paper provides evidence of and outlines the possible reasons that the peer review process is substandard in developing countries.

DISSEMINATED HISTOPLASMOSIS IN A PATIENT WITH NEWLY DIAGNOSED AIDS

TOPIC: Chest Infections TYPE: Medical Student/Resident Case Reports INTRODUCTION: Disseminated Histoplasmosis (DH) is an AIDS-defining illness caused by the dimorphic fungus Histoplasma capsulatum. Outbreaks have been associated with exposure to bird or bat droppings and amongst construction workers. It remains unclear whether DH represents an acute infection or a reactivation of latent infection. We present a case of DH in a newly diagnosed AIDS patient. CASE PRESENTATION: A 50 year old male Hispanic construction worker presented with a month history of persisting fever, chills, diaphoresis, progressive shortness of breath on exertion, non-bloody diarrhea and 15lbs weight loss. HIV screen was positive (new diagnosis) and his CD4+ cell count was 3 per cubic millimeter with a viral load of over 1 million copies/ml. CXR showed diffuse interstitial infiltrates in both lung fields and CT chest showed numerous punctate miliary pattern pulmonary nodules in the lungs with necrotic appearing lymph nodes in the proximal jejunal mesentery. SARS-CoV2 PCR was negative. BAL culture grew Histoplasma capsulatum, Lung biopsy pathology showed broad based budding yeast and urine histoplasma antigen was positive at greater than 23 ng/ml. He was treated with highly active antiretroviral therapy (HAART), IV liposomal amphotericin, and steroid. Empiric anti-TB therapy was stopped with negative quantiferon TB gold, BAL AFB smear and BAL MTB complex PCR. Silver stain for PCP, serum cryptococcal antigen, serum galactomammanan and fungitell assays were all negative. Hospital course was complicated by pneumothorax, septic shock, line related bloodstream infections that resolved with line removal and antimicrobials. Despite appropriate antifungal therapy for 40 days with decrease in his urine histoplasma antigen to 11 ng/ml, and HIV viral load decreasing to 330 copies/ml after 3 weeks of HAART, he remained ventilator dependent, on chest tubes and could not be weaned off sedation. His family made him comfort care only on hospital day 43 and he died peacefully after. DISCUSSION: Histoplasmosis has been recognized as an opportunistic infection in patients with AIDS and typically presents as disseminated disease. DH in conjunction with HIV infection is particularly common among Hispanic persons in the United states. In AIDS patients, DH is associated with a nonspecific clinical presentation—usually unexplained fever and weight loss. Histoplasmosis causes significant morbidity and mortality. Fungal infections deaths in AIDS were estimated at more than 700, 000 deaths (47%) annually. The frequent occurence of histoplasmosis with other opportunistic infections especially tuberculosis requires that tuberculosis be ruled out even if histoplasmosis is diagnosed. CONCLUSIONS: This case highlights the fact that although miliary pattern on CT Chest typically signifies tuberculosis, it can also be seen in histoplasmosis. Also associated morbidity and mortality of DH remains high in AIDS patients not on HAART. REFERENCE #1: Rana A. Hajjeh. Disseminated Histoplasmosis in Persons Infected with Human Immunodeficiency Virus. Clinical Infectious Diseases 1995; 21(Suppl 1):S108 -10. REFERENCE #2: Stuart M. Levitz, and Eugene J. Mark. Case 38-1998 — A 19-Year-Old Man with the Acquired Immunodeficiency Syndrome and Persistent Fever. N Engl J Med 1998; 339:1835-1843. REFERENCE #3: David W. Denning. Minimizing fungal disease deaths will allow the UNAIDS target of reducing annual AIDS deaths below 500 000 by 2020 to be realized. Philos Trans R Soc Lond B Biol Sci. 2016 Dec 5;371(1709). DISCLOSURES: No relevant relationships by Oluwadamilola Adeyemi, source=Web Response No relevant relationships by Ingrid Gils, source=Web Response No relevant relationships by Drew Ludwig, source=Web Response No relevant relationships by Biana Modilevsky, source=Web Response

An annotated bibliography of the printed works of James Petiver (c.1663–1718)

The works of James Petiver have a complicated publishing history. Apart from his more substantial publications, Musei Petiveriani (1695–1703) and Gazophylacii naturæ et artis (1702–1711), which were chiefly based on specimens in his collection and were issued in multiple parts, Petiver also published nearly thirty shorter articles and tracts, some of them merely hand-bills. Many of these publications were produced in small numbers and are scarce in their original imprints. However, long after Petiver’s death, James Millan published two editions (in 1764 and 1767) of Petiver’s work which were assembled partly from unsold copies of the originals, and partly through re-setting and abridging others that were otherwise unavailable. Petiver also contributed 35 articles to the Philosophical Transactions of the Royal Society and has previously been acknowledged as the author of a further four for The Monthly Miscellany: or, Memoirs for the Curious, a rare, short-lived periodical whose contributors were generally anonymous. However, this study concludes that nearly 50 additional articles that appeared in this journal between 1707 and 1710 were written by Petiver, several of which are the original versions of articles which were published in a re-set format by Millan in 1767. In other cases, articles first published there prove to be the basis for expanded accounts that Petiver published subsequently. An additional article was published in a similarly rare periodical, Memoirs of Literature, in 1714. All 158 of his published articles, wherever they appeared, are listed and indexed, and cross-references are provided where articles appear in more than one version.

Blood Transfusion and Venous Cannulation — Medical Publication and Innovation Across 350 Years of History

Abstract This article reviews historical milestones during the last 350 years starting with early experiments in intravenous injections of drugs and blood transfusion conducted in a climate of scientific discovery rather than clinical application. Technical problems encountered during attempts of vascular cannulation and a lack of knowledge of physiology resulted in complications related to intravenous access, sometimes fatal, which resulted in a complete ban on blood transfusion in Europe for 150 years. Meticulous documentation of these first 17th century experiments was published in Britain, in the “Philosophical Transactions of the Royal Society of London,” the oldest continuously published scientific journal still in existence, and in France, in the “Journal des Sçavans.” These journals became the primary means of communication of scientific research and letters amongst the community of scientists. Intravenous therapy marked the start of the first primitive anesthetic and laid the foundations for anesthesia and blood transfusion, although their clinical application came centuries later. Successful intravenous anesthesia was established around the turn of the 19th century. Brave men in the 17th century endeavored to awaken the spirit of inquiry and research among their peers at the Royal Society of London. Thanks to these bold medical men acting at a time of accelerated change, there was a great impact on clinical practice in many medical fields. Anesthesia now bears the fruits of these initial experiments so that, ultimately, anesthetists can provide safe and effective anesthesia while delivering anesthetic drugs, intravenous fluids, and blood transfusions for the benefit of patients.

A Bracing Nonlinear Walk in Applied Mechanics: Memoirs and Reflections

This article is an informal auto-biographical memoir by Mike Thompson, reflecting in retirement on his scientific researches in nonlinear phenomena, wandering pictorially from shell buckling, through bifurcations and chaos to climate tipping points. Some ideas and advice to young researchers are offered whenever it seems appropriate. Two research groups at University College London, and their two IUTAM Symposia are given some prominence, as are the ten years editing the Philosophical Transactions of the Royal Society.

New Identities in Peer Review: Who Are They and Why Are They Important?

Exalted by some people and criticized by others, since the peer review system has been implemented in scholarly journals it has transformed into an effective tool to select manuscripts of scientific merit for publication. Henry Oldenburg, the first Secretary of the Royal Society and creator of the Philosophical Transactions of the Royal Society (founded 1665), was one of the pioneers in implementing peer review in scientific journals. He started the peer-review system in Philosophical Transactions of the Royal Society by inviting 3 members of the Royal Society “who had more knowledge of the matters in question than he, to comment on submissions prior to making the decision about whether to publish.”1 At that time, the development of the peer-review system was linked to the concerns of scientists as science producers and consumers.2 As science producers, they wanted to have their work recognized by publishing in spaces valued by other members of the scientific community. As science consumers, they wanted to make sure that the studies elaborated by other scientists were evaluated with competence.2 The decisions taken by Oldenburg and the Council of the Royal Society to evaluate the quality of the content published in the Philosophical Transactions of the Royal Society constituted the foundations of peer review.2 Throughout the history of scholarly publishing, the peer-review process has typically been done by a small community of peers. These peers are defined in literature as “experienced researchers”3 and selected by the editors based on criteria such as academic seniority, academic degree, involvement […]

English engineer John Smeaton's experimental method(s): Optimisation, hypothesis testing and exploratory experimentation

In this paper I provide a detailed account of eighteenth-century engineer John Smeaton's experimental methods, with the aim of bringing our understanding of his work into line with recent research in the history and philosophy of science. Starting from his use of the technique of parameter variation, I identify three distinct methodological aims in the research he carried out on waterwheels, windmills and hydraulic mortars. These aims are: optimisation, hypothesis testing and maxim generation. The main claim of this paper is that Smeaton did more than merely improve engineering methods by systematising earlier artisanal approaches, which is the classic view of Smeaton's method developed by historians of technology in the 1990s. I argue instead that his approach bridged the divide between science and technology, by integrating both hypothesis testing and exploratory experimentation. This is borne out, in particular, by the way that Smeaton emphasised the exploratory side of the work he published in the Philosophical Transactions, in contrast to his account of the construction of the Eddystone lighthouse, which was aimed at a broader, non-specialist public. I contribute to recent research on exploratory experimentation by showing – in line with other work on this topic – that exploratory experimentation is not incompatible with hypothesis testing. This new perspective on Smeaton's method will hopefully lead to further research and new insights into the relation between science and technology at the start of the Industrial Revolution.

Turbulent periods and the development of the scientific research article, 1735–1835

Abstract The results of a previous study (Banks 2018) suggest that the development of scientific writing is more conservative in times of great turbulence. In an attempt to verify this, samples were taken from the Mémoires de l’Académie des Sciences and the Philosophical Transactions for the years 1735, 1785 and 1835. The development over the years 1735 to 1785 was compared to that between 1785 and 1835. Analysis of the grammatical functions and semantic categories of themes and of process types indicates that there is some evidence in favour of the conjecture that scientific writers are more conservative in times of turbulence. Whilst this is not conclusive, it suggests that further research would be fruitful.

Reprint: Translating the academic article in the late 17th century

The first academic periodical was the Journal des Sçavans whose first issue appeared in Paris in January 1665. This was followed two months later by the Philosophical Transactions in London. The Journal des Sçavans covered the whole range of academic disciplines and was made up mainly of book reviews. The Philosophical Transactions was restricted to science and technology and was based on the contents of the editor's correspondence. The academic communities in France and England were in contact and aware of each other's activities. The first issue of the Philosophical Transactions includes an item translated from the first issue of the Journal des Sçavans. Previous study, including consideration of thematic structure and process types, has shown that the English translator follows the French text fairly closely. The first translation from English to French appears in the following year. In this case the translator is highly selective in choosing those parts of the original text to include in his French version. The present study looks at the situation 10 years later. In 1675, the Philosophical Transactions produced 11 issues, including a number of translations, two of which were translated from the Journal des Sçavans. The latter periodical produced 23 issues including 10 items translated from the Philosophical Transactions, three of which have been randomly selected for his study. It is found that the strategies used in the first translations are maintained here: the English translator follows the French text closely, while the French translator uses a strategy of selective translation. It is hypothesized that the French translators are adapting the text for a different type of readership, which might be seen as an early form of localization.

Scientific research trends in gifted individuals with autism spectrum disorder: A Bibliographic Scattering Analysis (1998-2020)

ABSTRACT This study used the bibliographic scattering analysis to explore the scientific publications trends on gifted individuals with autism spectrum disorders (ASD) over the past 23 years. The study examined the applicability and appropriateness of Bradford’s and Lotka’s laws of scattering to measure the impact factors of journals, institutions, countries, researchers, and personal publications on the area of research. After examining 95 research papers published in 55 Social Sciences Citation Indexed (SSCI) journals from 1998 to 2020. The rank list was prepared to identify the core journals in education. Themost frequent venues of journals in descending order of times cited are, Philosophical Transactions of the Royal Society B-Biological Science (USA) with 33.8% of citation, followed by the Journal of Autism and Developmental Disorders (USA) with 10.3% of citation and Journal of the American Academy of Child and Adolescent Psychiatry (USA) with 8.2% of citation. The top four categories of research were psychology with 37.13% of publications, followed by psychiatry (13.77%), neurosciences and neurology (11.38%), and education (8.38%). The study found that Asperger syndrome (AS) is still used in academic studies, even after it was immersed in the ASD by DSM-5 criteria. The findings and limitations were presented and discussed.

Analysis of the IgA Heavy Chain Repertoire in Multiple Myeloma: Implications for Host-Microbiome Influences

Background: Advances in understanding the biology of multiple myeloma (MM) have translated into novel treatment paradigms that have prolonged survival. Nevertheless, relapse remains common even in the absence of measurable residual disease. Therefore, further research is required to identify additional mechanisms underlying MM pathogenesis, particularly in high-risk subtypes. IgA MM represents approximately 20% of cases and for unclear reasons confers a worse prognosis. Given the physiologic inter-relationships of host IgA with microbiota, we first characterized IgA levels in MM patients and then used a highly sensitive next generation sequencing (NGS) technique for genetic-structural analyses to provide possible insights into selection biases in IgA heavy chain usage that may suggest common antigenic exposures.Methods: Total RNA was obtained from unsorted peripheral blood (PB) and bone marrow (BM) mononuclear cells from 14 newly diagnosed MM patients, as well as PB from 9 healthy controls. A heavy chain isotype-specific ELISA was used to characterize serum IgA levels. For highly sensitive unbiased IgA antibody gene repertoire surveys, we developed a PCR-based technique (El Bannoudi et al. Methods Mol Biol. 2017) using 5'-rapid amplification of cDNA ends to amplify the IgA heavy chain rearrangements for MiSeq (Illumina, San Diego, CA) next generation sequencing (NGS). Immunoglobulin heavy chain (IGH) VH, DH and JH sequences were aligned to their corresponding germline alleles using IgSCUEAL, a previously described sequence alignment algorithm (Frost et al. Philos Trans R Soc Lond B Biol Sci. 2015). To quantify stool microbiota bound to serum IgA, FACS analysis with human anti-IgA-Fc secondary antibodies (Abcam, Cambridge, MA) was performed using primary antibodies from MM or control serum mixed with stool from the same individual.Results: In healthy adults, IgA1 predominates 4-fold in the circulation compared to IgA2 which is produced mostly in the mucosa, yet more extreme skewing was found in IgA1 in MM patients, with suppression of serum IgA2 as assessed by ELISA. For NGS, there was a mean 2.1x105 sequences read which identified an estimated 7.4 x105 clonotypes, with highly reproducible results among technical replicates. When comparing PB to BM compartments, there were differences in the dominant IgA repertoires, particularly in IgA MM where PB showed a preponderance of a VH3-JH5 (mostly VH3-74) clone. In PB the majority of IGH sequences were derived from subclones of VH1, VH3, and VH4, and JH1, JH4, and JH5 clones, whereas in BM VH1, VH3 and JH4, JH5 subclones predominated. These were distinct from the PB repertoires of healthy controls. Lastly, pilot experiments quantifying IgA bound to stool bacteria using MM serum antibodies and FACS analysis yielded nearly 11-fold total cells, compared to results from a parallel experiment in a healthy control (2.7x106 vs 2.3x105 cells, respectively). Ongoing work is aimed at commensal taxa determination of sorted cells using 16S rRNA sequencing.Conclusions: We present initial studies that reveal alterations of the total IgA heavy chain repertoire in IgA MM using an unbiased NGS technique, which can suggest influences on B cell selection during clonal evolution. These preliminary studies show that distinct disease-related and background IgA heavy chain repertoires exist in MM compared to healthy individuals. Future analyses are aimed at clustering IgA heavy chain sequences into clonal subsets to define their evolution from MM precursors. In addition, differences in the degrees of IgA-bound gut flora compared to a healthy individual suggest dysbiosis in the MM microbiome, warranting further investigation. DisclosuresNo relevant conflicts of interest to declare.

A cracking approach to inventing new tough materials: fracture stranger than friction.

A cracking approach to inventing new tough materials: fracture stranger than friction.

Simultaneously Improving Solution Processing and Electronic Doping in Carbon Nanotube Thermoelectrics

Thermoelectrics are solid state devices that convert waste heat into electricity. Their abundancy and low toxicity makes carbon materials good candidates for thermoelectric applications requiring large areas and operation at low to medium temperatures [1]. Carbon nanotubes (CNTs) offer generally good electrical conductivity, which is a must for thermoelectrics. While their Seebeck coefficient can also be high, it has been shown to decrease as the conductivity increases. Optimum performance, therefore, requires a fine tuned doping level in order to find the sweet spot. On the other side, CNTs are often difficult to process, which may limit its applicability for this type of applications.In this invited talk, I will present two different strategies that our group is using in order to simultaneously improve processing capabilities and control doping level. First we will discuss the use of composites of CNTs and highly soluble polymers. Electron withdrawing or donating polymers, such as PEI and P3HT, respectively, help disperse the CNTs and simultaneously dope the CNT p- or n-type [2,3]. Alternatively, the use of bacteria to produce composites of cellulose and CNTs provides additional means of producing high performing composites [4]. Finally, I will describe our latest work on the use of alkali metals to form real CNT solutions and simultaneously produce stable n-doping of the resulting buckypapers [5].[1] Will organic thermoelectrics get hot? M. Campoy-Quiles, Philosophical Transactions of the Royal Society A, 377, 20180352 (2019).[2] Photoinduced p- to n-type Switching in Thermoelectric Polymer-Carbon Nanotube Composites, B. Dörling, J. D. Ryan, J. D. Craddock, A. Sorrentino, A. El Basaty, A. Gomez, M. Garriga, E. Pereiro, J. E. Anthony, M. C. Weisenberger, A. R. Goñi, C. Müller and M. Campoy-Quiles, Advanced Materials, 28, 2782 (2016).[3] Investigating thermoelectric stability under encapsulation using PEI‐Doped CNT films as a model system, F. Abdallah, L. Ciammaruchi, A. Jiménez‐Arguijo, E.S.M. Duraia, H.S. Ragab, B. Dörling and M. Campoy‐Quiles, Advanced Materials Technologies, 5, 2000256 (2020).[4] Farming thermoelectric paper, D. Abol-Fotouh, B. Dörling, O. Zapata-Arteaga, X. Rodríguez-Martínez, A. Gómez, J. S. Reparaz, A. Laromaine, A. Roig and M. Campoy-Quiles, Energy and Enviromental Science, 12, 716-726 (2019).[5] Soluble Alkali-Metal CNT Salts for n-type Thermoelectric Composites, B. Dörling, X. Rodríguez-Martínez, I. Álvarez-Corzo, M. Campoy-Quiles, submitted (2021).

Celebrating Women in Paleobotany: A Tribute to Edith L. Taylor—Introduction and Dedication

Celebrating Women in Paleobotany: A Tribute to Edith L. Taylor—Introduction and Dedication

Long wavelength streamwise vortices caused by wall curvature or roughness

Long wavelength instabilities of boundary layers caused by centrifugal effects or wall roughness are investigated. The wall roughness is modelled by small amplitude surface waviness. The instability is described in the nonparallel regime where it develops on the same length scale as the unperturbed flow. It is shown that instabilities initiated by disturbances close to the leading edge initially deform rapidly into algebraically growing eigensolutions but then deform into exponentially growing disturbances. The disturbances ultimately develop in a quasi-parallel manner and then pass successively through the high Gortler number, or equivalent large roughness parameter, regimes first described by Denier et al. (Nasa Contractor ICASE Report 90-31, 1990; Philos Trans R Soc A 334:51–85, 1991). It is shown that the mode which develops downstream is the most rapidly growing one available and not the second most unstable mode as claimed in a recent paper.

Uniform Asymptotics of Toeplitz Determinants with Fisher\u2013Hartwig Singularities

We obtain an asymptotic formula for ntimes n Toeplitz determinants as nrightarrow infty , for non-negative symbols with any fixed number of Fisher–Hartwig singularities, which is uniform with respect to the location of the singularities. As an application, we prove a conjecture by Fyodorov and Keating (Philos Trans R Soc A 372: 20120503, 2014) regarding moments of averages of the characteristic polynomial of the Circular Unitary Ensemble. In addition, we obtain an asymptotic formula regarding the momentum of impenetrable bosons in one dimension with periodic boundary conditions.

What it Might Be like to Be a Group Agent

Many theorists have defended the claim that collective entities can attain genuine agential status. If collectives can be agents, this opens up a further question: can they be conscious? That is, is there something that it is like to be them? Eric Schwitzgebel (Philosophical Studies 172: 1697–1721, 2015) argues that yes, collective entities (including the United States, taken as a whole), may well be significantly conscious. Others, including Kammerer (Philosophia 43: 1047–1057, 2015), Tononi and Koch (Philosophical Transactions of the Royal Society B: Biological Sciences 370: 20140167–20140167, 2015) , and List (Nous 52: 295–319, 2018) reject the claim. List does so on the basis of Tononi’s Integrated Information Theory of consciousness (Encyclopedia of Consciousness, 403–416, 2009). I argue here that List’s rejection is too quick, and that groups can, at least in principle, display the kind of informational integration we might think is necessary for consciousness. However, group consciousness will likely differ substantially from the individual experiences that give rise to it. This requires the defender of group consciousness to face up to a similar combination problem as the panpsychist.

Henry Oldenburg and a Brief Notice of Milton’sOf Educationin thePhilosophical Transactions

Henry Oldenburg and a Brief Notice of Milton’s<i>Of Education</i>in the<i>Philosophical Transactions</i>

Diffusion-based degeneration of the collagen reinforcement in the pathologic human cornea

We describe a multiphysics model of the collagen structure of the cornea undergoing a progressive localized reduction of the stiffness, preluding to the development of ectasia and keratoconus. The architecture of the stromal collagen is assumed to follow the simplified two-family model proposed in Pandolfi et al. (A microstructural model of cross-link interaction between collagen fibrils in the human cornea. Philos Trans R Soc A 377:20180079, 2019), where the mechanical stiffness of the structure is supplied by transversal bonds within the fibrils of the same family (inter-crosslink bonds) and across the fibrils of the two families (intra-crosslink bonds). In Pandolfi et al. (A microstructural model of cross-link interaction between collagen fibrils in the human cornea. Philos Trans R Soc A 377:20180079, 2019), it was shown that the loss of the spherical shape due to the protrusion of a cone can be ascribed to the mechanical weakening of the intra-crosslink bonds in the central region of the collagen structure. In the present study, the reduction of bond stiffness is coupled to an evolutive pathologic phenomenon, modeled as a reaction–diffusion process of a normalized scalar field. We assume that the scalar field is a concentration-like measure of the degeneration of the chemical bonds stabilizing the structural collagen. We follow the evolution of the mechanical response of the system in terms of shape change, according to the propagation of the degeneration field, and identify the critical loss of mechanical stability resulting in the typical bulging of keratoconus corneas.

Translating the English academic article for a French readership in 1686

AbstractPrevious studies of translations from thePhilosophical Transactionsto theJournal des Sçavansin 1665 and 1675 showed that the translators adopted a strategy of selective translation. The present study looks at five examples published in 1686. Selective translation is again in evidence. Analyses of thematic structure and process types, however, show only slight differences, but with biases towards constant progression and material processes in the French versions. It is suggested that this can be explained by the translator adapting his texts to his readership. Whereas thePhilosophical Transactionswas restricted to questions of science and technology, theJournal des Sçavansdealt with all the academic disciplines of the time, and thus had a wider readership than its English counterpart.