bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep unsupervised learning using spike-timing-dependent plasticity
Authors: Lu Sen , Sengupta Abhronil 
Published: April 2024

Abstract
Spike-timing-dependent plasticity (STDP) is an unsupervised learning mechanism for spiking neural networks that has received significant attention from the neuromorphic hardware community. However, scaling such local learning techniques to deeper networks and large-scale tasks has remained elusive. In this work, we investigate a Deep-STDP framework where a rate-based convolutional network, that can be deployed in a neuromorphic setting, is trained in tandem with pseudo-labels generated by the STDP clustering process on the network outputs. We achieve 24.56% higher accuracy and 3.5 × faster convergence speed at iso-accuracy on a 10-class subset of the Tiny ImageNet dataset in contrast to a k-means clustering approach.
Causal-ARG: a causality-guided framework for annotating properties of antibiotic resistance genes
Authors: Zhao Weizhong , Wu Junze , Jiang Xingpeng , He Tingting , Hu Xiaohua 
Published: April 2024

Abstract

Motivation
The crisis of antibiotic resistance, which causes antibiotics used to treat bacterial infections to become less effective, has emerged as one of the foremost challenges to public health. Identifying the properties of antibiotic resistance genes (ARGs) is an essential way to mitigate this issue. Although numerous methods have been proposed for this task, most of these approaches concentrate solely on predicting antibiotic class, disregarding other important properties of ARGs. In addition, existing methods for simultaneously predicting multiple properties of ARGs fail to account for the causal relationships among these properties, limiting the predictive performance.

Results
In this study, we propose a causality-guided framework for annotating properties of ARGs, in which causal inference is utilized for representation learning. More specifically, the hidden biological patterns determining the properties of ARGs are described by a Gaussian Mixture Model, and procedure of causal representation learning is used to derive the hidden features. In addition, a causal graph among different properties is constructed to capture the causal relationships among properties of ARGs, which is integrated into the task of annotating properties of ARGs. The experimental results on a real-world dataset demonstrate the effectiveness of the proposed framework on the task of annotating properties of ARGs.

Availability and implementation
The data and source codes are available in GitHub at https://github.com/David-WZhao/CausalARG.
VarChat: the generative AI assistant for the interpretation of human genomic variations
Authors: De Paoli Federica , Berardelli Silvia , Limongelli Ivan , Rizzo Ettore , Zucca Susanna 
Published: April 2024

Abstract

Motivation
In the modern era of genomic research, the scientific community is witnessing an explosive growth in the volume of published findings. While this abundance of data offers invaluable insights, it also places a pressing responsibility on genetic professionals and researchers to stay informed about the latest findings and their clinical significance. Genomic variant interpretation is currently facing a challenge in identifying the most up-to-date and relevant scientific papers, while also extracting meaningful information to accelerate the process from clinical assessment to reporting. Computer-aided literature search and summarization can play a pivotal role in this context. By synthesizing complex genomic findings into concise, interpretable summaries, this approach facilitates the translation of extensive genomic datasets into clinically relevant insights.

Results
To bridge this gap, we present VarChat (varchat.engenome.com), an innovative tool based on generative AI, developed to find and summarize the fragmented scientific literature associated with genomic variants into brief yet informative texts. VarChat provides users with a concise description of specific genetic variants, detailing their impact on related proteins and possible effects on human health. In addition, VarChat offers direct links to related scientific trustable sources, and encourages deeper research.

Availability and implementation
varchat.engenome.com.
Queer and trans community building in post-NALSA and post-377 India: a critical reflection
Authors: Kumar Pushpesh , Datta Sayantan , Mishra Neha 
Published: April 2024

Abstract
This article reflects on contestations that mark queer and trans community building in post- National Legal Services Authority (NALSA) and post-377 India. In the past decade, queer and trans communities in India have witnessed two landmark judgements: the NALSA v. Union of India judgement 2014 and the Navtej Singh Johar and Ors. v. Union of India judgement 2018. The former granted transgender persons legal recognition and a promise of civil and substantive rights. The latter read down the draconian Sec. 377 of the Indian Penal Code that criminalized consensual adult homosexual sex acts. In light of these two judgements, this article traces challenges faced by queer and trans communities and challenges to queer and trans community building in contemporary India by tracing recent developments in the contexts of health, public policy, jurisprudence, social institutions, education, popular culture, and the precarity of gender and sexually transgressive communities during the recent COVID-19 pandemic. Finally, the authors also trace narratives of hope that demonstrate how queer and trans people in post legal reform India continue to build enabling and affirmative communities in the face of an increasingly neoliberalizing country.
Skin dermatoses in the returning traveller: a practical guide
Authors: Efstathiadou Anthoula , Tsourouktsoglou Harilena , Shipman Alexa R 
Published: April 2024

Abstract
Skin problems are common in returning travellers, despite the fact that vaccination, insect repellent techniques, adequate clothing and footwear are all ways to prevent skin disease. When travelling to unusual areas, the traveller can still expect to pick up diseases that are common across the world, such as lice, scabies, and staphylococcal or streptococcal infections. What can differ are the different arthropods and the diseases they can spread. Given the plethora of dermatoses in returning travellers, a methodological approach is necessary. We attempted such an approach by creating a practical guide that includes a diagnostic flowchart alongside a world map presenting common skin problems by continent. Additional information regarding possible investigations, along with tables presenting common infectious skin diseases and their corresponding presentations, is also included in our study. Our aim is to help clinicians approach skin dermatosis in patients returning from holidays, acknowledging the diagnostic difficulties that this might entail.
Primary hyperoxaluria in adults and children: a nationwide cohort highlights a persistent diagnostic delay
Authors: Pszczolinski Romain , Acquaviva Cécile , Berrahal Insaf , Biebuyck Nathalie , Burtey Stéphane , Clabault Karine , Dossier Claire , Guillet Matthieu , Hemery Floriane , Letavernier Emmanuel , Rousset-Rouvière Caroline , Bacchetta Justine , Moulin Bruno 
Published: April 2024

ABSTRACT

Background
Primary hyperoxalurias (PH) are extremely rare genetic disorders characterized by clinical heterogeneity. Delay in diagnosing these conditions can have detrimental effects on patient outcomes. The primary objective of this study is to assess the current diagnostic delay for PH.

Methods
This nationwide, observational and retrospective study included patients who received a genetic diagnosis of PH types 1, 2 and 3 between 1 January 2015 and 31 December 2019. Diagnostic delay was defined as the duration between the onset of symptoms and the time of genetic diagnosis.

Results
A total of 52 patients (34 children and 18 adults) were included in the study, with 40 PH1 (77%), 3 PH2 (6%) and 9 PH3 (17%). At the time of diagnosis, 12 patients (23%) required dialysis. Among the PH1 patients, the predominant symptom at onset in adults was renal colic (79% of cases), whereas symptoms in children were more diverse (renal colic in 17% of cases). The diagnostic delay was significantly shorter in children compared with adults [median (interquartile range)]: 1.2 (0.1–3.0) versus 30 (17–36) years, respectively (P &lt; .0001). RNA interference was utilized in 23 patients (58%). Five individuals (13%) underwent double liver–kidney transplantation, and five (13%) received isolated kidney transplantation, with lumasiran therapy in four patients. For PH2 and PH3 patients, the diagnostic delay ranges from 0 to 3 years, with renal colic as first symptom in 33% of cases.

Conclusion
This extensive and recent cohort of PH underscores the considerable delay in diagnosing PH, particularly in adults, even in a country with a dedicated organization for enhancing the overall management of rare diseases. These findings reinforce the imperative for increased awareness among relevant specialties regarding the evaluation of urolithiasis.
Dapagliflozin treatment of patients with chronic kidney disease without diabetes across different albuminuria levels (OPTIMISE-CKD)
Authors: Svensson Maria K , Tangri Navdeep , Bodegård Johan , Adamsson Eryd Samuel , Thuresson Marcus , Sofue Tadashi 
Published: April 2024

ABSTRACT

Background
We compared kidney and cardiorenal protection in patients without type 2 diabetes across urine albumin–creatinine ratio (UACR) levels after initiation on dapagliflozin for the treatment of chronic kidney disease (CKD).

Methods
OPTIMISE-CKD is an observational study describing dapagliflozin treatment for CKD. Adult patients with CKD without type 2 diabetes were included in the primary analysis. Baseline UACR was grouped as normal/mildly elevated (0–29 mg/g), low (30–200 mg/g) and high (&gt;200 mg/g). Outcomes were estimated glomerular filtration rate (eGFR) trajectories/slopes, cardiorenal complications and all-cause mortality.

Results
In total, 1480 patients had low (n = 796) and high (n = 684) UACR. The two groups were similar at baseline, aged 75 and 74 years, and 42% and 39% female, respectively. After dapagliflozin initiation, an acute eGFR dip of 3 mL/min/1.73 m2 was observed, followed by a flat development in both groups. The eGFR slope [95% confidence interval (CI)] for patients with low UACR was 0.79 mL/min/1.73 m2 per year (–0.59, 2.56), and similar to patients with high UACR [0.40 mL/min/1.73 m2 per year (–0.46, 1.38)]. Risks of cardiorenal complications and all-cause mortality were similar, with adjusted hazard ratios of 0.89 (95% CI 0.66, 1.19) and 1.10 (95% CI 0.63, 1.92), respectively. Analogous results were found in those with normal/mildly elevated UACR.

Conclusions
Dapagliflozin in patients without type 2 diabetes for the treatment of CKD demonstrated similar kidney protection, cardiorenal and all-cause mortality risk across UACR levels. This suggests that the efficacy of dapagliflozin found in clinical trials expands to real-world patients with CKD, regardless of albuminuria levels.
Disability and Superability: The Spectacle of Extra/Ordinary Bodies in Maxine Hong Kingston’sTripmaster Monkey: His Fake Book
Authors: Chen Fu-jen 
Published: April 2024

AbstractThis essay explores how Maxine Hong Kingston’s Tripmaster Monkey (1989) showcases and anticipates cultural imaginaries surrounding Asian bodies as repositories for fantasy and affect. From the fragmented body of the suicidal protagonist to the spectacle of the Siamese conjoined twins, Kingston stages diverse bodily tropes that reflect racist, sexist, and ableist perceptions throughout history. The protagonist Wittman Ah Sing, embodied as a postmodern “Monkey King,” represents a neoliberal subjectivity marked by adaptive resilience. In contrast, the Siamese twins enact intersubjective connections, catalyzing the protagonist’s communal theater production. The play’s communal vision challenges the ideological norms of the “Normate” and resists complicity with global capitalism. Ultimately, the acknowledgment of shared struggles amidst radical divisions and recognition of our participation in ideological fantasies fosters collective solidarity and a radical critique of the capitalist system.
‘William Fowler’, Sir William Garrard, Sir John Hawkins and the Sixteenth-Century Atlantic Slave Trade
Authors: Baker Gary Paul , Lambert Craig 
Published: April 2024

Abstract
This article sheds new light on English involvement in the sixteenth-century transatlantic slave trade, especially the voyages of John Hawkins in the 1560s. Its focus is on William Fowler, a merchant who in 1569 was brought in front of the English High Court of the Admiralty to provide expert evidence on behalf of Sir William Garrard and Sir John Hawkins. Fowler was an experienced slave trader who worked within the Spanish system, probably trading out of Seville to New Spain. His testimony in 1569 was of great importance to Hawkins, Garrard and the other investors who backed Hawkins’s ill-fated slaving voyage of 1567–9, for in his testimony Fowler provided independent and up-to-date information as to the value of slaves and other commodities which Hawkins lost in 1568 at San Juan de Ulúa. Hawkins and his backers would use these valuations to bolster their claim for compensation from the Spanish Crown for the goods they lost in 1568. Using previously unpublished sources, the article will investigate the origins of William Fowler and assess the social and economic connections that existed between Hawkins and his investors, and explain why these socio-economic networks brought Fowler to the Admiralty court in 1569. The article concludes with a transcription of Fowler’s testimony.
Bendopnea prevalence and prognostic value in older patients with heart failure: FRAGILE-HF–SONIC-HF post hoc analysis
Authors: Nakade Taisuke , Maeda Daichi , Matsue Yuya , Fujimoto Yudai , Kagiyama Nobuyuki , Sunayama Tsutomu , Dotare Taishi , Jujo Kentaro , Saito Kazuya , Kamiya Kentaro , Saito Hiroshi , Ogasahara Yuki , Maekawa Emi , Konishi Masaaki , Kitai Takeshi , Iwata Kentaro , Toki Misako , Yoshioka Kenji , Wada Hiroshi , Kasai Takatoshi , Nagamatsu Hirofumi , Momomura Shin-ichi , Minamino Tohru 
Published: April 2024

Abstract

Aims
This study aimed to investigate the prevalence, clinical characteristics, and prognostic value of bendopnea in older patients hospitalized for heart failure.

Methods and results
This post hoc analysis was performed using two prospective, multicentre, observational studies: the FRAGILE-HF (main cohort) and SONIC-HF (validation cohort) cohorts. Patients were categorized based on the presence of bendopnea, which was evaluated before discharge. The primary endpoint was 2-year all-cause mortality after discharge. Among the 1243 patients (median age, 81 years; 57.2% male) in the FRAGILE-HF cohort and 225 (median age, 79 years; 58.2% men) in the SONIC-HF cohort, bendopnea was observed in 31 (2.5%) and 10 (4.4%) patients, respectively. Over a 2-year follow-up period, all-cause death occurred in 20.8 and 21.9% of the patients in the FRAGILE-HF and SONIC-HF cohorts, respectively. Kaplan–Meier survival curves demonstrated significantly higher mortality rates in patients with bendopnea than in those without bendopnea in the FRAGILE-HF (log-rank P = 0.006) and SONIC-HF cohorts (log-rank P = 0.014). Cox proportional hazard analysis identified bendopnea as an independent prognostic factor for all-cause mortality in both the FRAGILE-HF [hazard ratio (HR) 2.11, 95% confidence interval (CI) 1.18–3.78, P = 0.012] and SONIC-HF cohorts (HR 4.20, 95% CI 1.63–10.79, P = 0.003), even after adjusting for conventional risk factors.

Conclusion
Bendopnea was observed in a relatively small proportion of older patients hospitalized for heart failure before discharge. However, its presence was significantly associated with an increased risk of all-cause mortality.
Ferriphaselus amnicola strain GF-20, a new iron- and thiosulfate-oxidizing bacterium isolated from a hard rock aquifer
Authors: Garry Mélissa , Farasin Julien , Drevillon Laetitia , Quaiser Achim , Bouchez Camille , Le Borgne Tanguy , Coffinet Sarah , Dufresne Alexis 
Published: April 2024

Abstract
Ferriphaselus amnicola GF-20 is the first Fe-oxidizing bacterium isolated from the continental subsurface. It was isolated from groundwater circulating at 20 m depth in the fractured-rock catchment observatory of Guidel-Ploemeur (France). Strain GF-20 is a neutrophilic, iron- and thiosulfate-oxidizer and grows autotrophically. The strain shows a preference for low oxygen concentrations, which suggests an adaptation to the limiting oxygen conditions of the subsurface. It produces extracellular stalks and dreads when grown with Fe(II) but does not secrete any structure when grown with thiosulfate. Phylogenetic analyses and genome comparisons revealed that strain GF-20 is affiliated with the species F. amnicola and is strikingly similar to F. amnicola strain OYT1, which was isolated from a groundwater seep in Japan. Based on the phenotypic and phylogenetic characteristics, we propose that GF-20 represents a new strain within the species F. amnicola.
Code-Switching, Queering Food and Narrative Construction in Monica Meneghetti’s Memoir What the Mouth Wants
Authors: Baldo Michela 
Published: April 2024

ABSTRACT
This article examines the extent to which the Italian-Canadian queer writer Monica Meneghetti, in her memoir What the Mouth Wants, challenges and disrupts heteronormative notions of gender and sexuality through the code-switching of food terms in Italian or in a Northern Italian dialect. Code-switching is used primarily to evoke memories of Meneghetti’s late mother through the author’s favourite dishes, and of the homophobia (or rather biphobia) directed at her by her father, with whom she used to make fresh pasta and cook Italian meals. The memories and flashbacks, interspersed with present-day accounts of the preparation of Italian childhood meals with her polyamorous family, allow the memoir’s protagonist to build a new sense of family: a queer Italian-Canadian family. Drawing on feminist and queer food studies, the article reveals that Meneghetti uses code-switching to signal point of view and to construct the memoir’s characters and plot, as code-switched food items are also linked to the notion of memory and to what it means to write the memoir.
Parthenogenetic Stick Insects Exhibit Signatures of Preservation in the Molecular Architecture of Male Reproduction
Authors: Forni Giobbe , Mantovani Barbara , Mikheyev Alexander S , Luchetti Andrea 
Published: April 2024

Abstract
After the loss of a trait, theory predicts that the molecular machinery underlying its phenotypic expression should decay. Yet, empirical evidence is contrasting. Here, we test the hypotheses that (i) the molecular ground plan of a lost trait could persist due to pleiotropic effects on other traits and (ii) that gene co-expression network architecture could constrain individual gene expression. Our testing ground has been the Bacillus stick insect species complex, which contains close relatives that are either bisexual or parthenogenetic. After the identification of genes expressed in male reproductive tissues in a bisexual species, we investigated their gene co-expression network structure in two parthenogenetic species. We found that gene co-expression within the male gonads was partially preserved in parthenogens. Furthermore, parthenogens did not show relaxed selection on genes upregulated in male gonads in the bisexual species. As these genes were mostly expressed in female gonads, this preservation could be driven by pleiotropic interactions and an ongoing role in female reproduction. Connectivity within the network also played a key role, with highly connected—and more pleiotropic—genes within male gonad also having a gonad-biased expression in parthenogens. Our findings provide novel insight into the mechanisms which could underlie the production of rare males in parthenogenetic lineages; more generally, they provide an example of the cryptic persistence of a lost trait molecular architecture, driven by gene pleiotropy on other traits and within their co-expression network.
WormBase 2024: status and transitioning to Alliance infrastructure
Authors: Sternberg Paul W , Van Auken Kimberly , Wang Qinghua , Wright Adam , Yook Karen , Zarowiecki Magdalena , Arnaboldi Valerio , Becerra Andrés , Brown Stephanie , Cain Scott , Chan Juancarlos , Chen Wen J , Cho Jaehyoung , Davis Paul , Diamantakis Stavros , Dyer Sarah , Grigoriadis Dionysis , Grove Christian A , Harris Todd , Howe Kevin , Kishore Ranjana , Lee Raymond , Longden Ian , Luypaert Manuel , Müller Hans-Michael , Nuin Paulo , Quinton-Tulloch Mark , Raciti Daniela , Schedl Tim , Schindelman Gary , Stein Lincoln 
Published: April 2024

Abstract
WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. elegans research, to provide better integration with other resources, and to be sustainable. Here, we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance member, WormBase will continue to interact with the C. elegans community, develop new features as needed, and curate key information from the literature and large-scale projects.
Repair of the complete atrioventricular septal defect—impact of postoperative moderate or more regurgitation
Authors: Ozturk Mahmut , Tongut Aybala , Sterzbecher Vanessa , Desai Manan , Esmailian Gabriel , Henmi Soichiro , Spurney Christopher , Staffa Steven J , d’Udekem Yves , Yerebakan Can 
Published: April 2024

Abstract

OBJECTIVES
To study the risk factors for mortality, moderate or more left atrioventricular valve regurgitation (LAVVR) and reoperation after the surgical repair of complete atrioventricular septal defect (cAVSD) in a single centre.

METHODS
The current study is a retrospective review of patients who underwent surgical repair of cAVSD between 2000 and 2021. Patients with unbalanced ventricles not amenable to biventricular repair, double outlet right ventricle and malpositioned great arteries were excluded. The clinical predictors of outcome for end points were analysed with univariate and multivariable Cox regression analysis or Fine–Gray modelling for competing risks. Time-dependent end points were estimated using the Kaplan–Meier curve analysis and cumulative incidence curves.

RESULTS
The median follow-up time was 2.3 years. Among 220 consecutive patients were 10 (4.6%) operative and 21 late mortalities (9.6%). A total of 26 patients were identified to have immediate postoperative moderate or more regurgitation and 10 of them ultimately died. By multivariable analysis prematurity and having more than moderate regurgitation immediately after the operation were identified as predictors of overall mortality (P = 0.003, P = 0.012). Five- and ten-year survival rates were lower for patients with immediate postoperative moderate or more LAVVR {51.9% [confidence interval (CI): 27.5–71.7%]} when compared to patients without moderate or more regurgitation [93.2% (CI: 87.1–96.4%) and 91.3% (CI: 83.6–95.5%)].

CONCLUSIONS
The patients who undergo cAVSD repair remain subjected to a heavy burden of disease related to postoperative residual LAVVR. Immediate postoperative moderate or more LAVVR contributes significantly to overall mortality. Whether a second run of bypass can decrease this observed mortality should be investigated.