bluuebunny/crossref_metadata_2025_split huggingface dataset:
Binary amplitude holograms for shaping complex light fields with digital micromirror devices
Authors: Gutiérrez-Cuevas R , Popoff S M 
Published: October 2024

Abstract
Digital micromirror devices are a popular type of spatial light modulators for wavefront shaping applications. While they offer several advantages when compared to liquid crystal modulators, such as polarization insensitivity and rapid-switching, they only provide a binary amplitude modulation. Despite this restriction, it is possible to use binary holograms to modulate both the amplitude and phase of the incoming light, thus allowing the creation of complex light fields. Here, a didactic exploration of various types of binary holograms is presented. A particular emphasis is placed on the fact that the finite number of pixels coupled with the binary modulation limits the number of complex values that can be encoded into the holograms. This entails an inevitable trade-off between the number of complex values that can be modulated with the hologram and the number of independent degrees of freedom available to shape light, both of which impact the quality of the shaped field. Nonetheless, it is shown that by appropriately choosing the type of hologram and its parameters, it is possible to find a suitable compromise that allows shaping a wide range of complex fields with high accuracy. In particular, it is shown that choosing the appropriate alignment between the hologram and the micromirror array allows for maximizing the number of complex values. Likewise, the implications of the type of hologram and its parameters on the diffraction efficiency are also considered.
Accelerating protein–protein interaction screens with reduced AlphaFold-Multimer sampling
Authors: Bellinzona Greta , Sassera Davide , Bonvin Alexandre M J J 
Published: October 2024

Abstract

Motivation
Discovering new protein–protein interactions (PPIs) across entire proteomes offers vast potential for understanding novel protein functions and elucidate system properties within or between an organism. While recent advances in computational structural biology, particularly AlphaFold-Multimer, have facilitated this task, scaling for large-scale screenings remains a challenge, requiring significant computational resources.

Results
We evaluated the impact of reducing the number of models generated by AlphaFold-Multimer from five to one on the method’s ability to distinguish true PPIs from false ones. Our evaluation was conducted on a dataset containing both intra- and inter-species PPIs, which included proteins from bacterial and eukaryotic sources. We demonstrate that reducing the sampling does not compromise the accuracy of the method, offering a faster, efficient, and environmentally friendly solution for PPI predictions.

Availability and implementation
The code used in this article is available at https://github.com/MIDIfactory/AlphaFastPPi. Note that the same can be achieved using the latest version of AlphaPulldown available at https://github.com/KosinskiLab/AlphaPulldown
Chain-aware graph neural networks for molecular property prediction
Authors: Wang Honghao , Zhang Acong , Zhong Yuan , Tang Junlei , Zhang Kai , Li Ping 
Published: October 2024

Abstract

Motivation
Predicting the properties of molecules is a fundamental problem in drug design and discovery, while how to learn effective feature representations lies at the core of modern deep-learning-based prediction methods. Recent progress shows expressive power of graph neural networks (GNNs) in capturing structural information for molecular graphs. However, we find that most molecular graphs exhibit low clustering along with dominating chains. Such topological characteristics can induce feature squashing during message passing and thus impair the expressivity of conventional GNNs.

Results
Aiming at improving node features’ expressiveness, we develop a novel chain-aware graph neural network model, wherein the chain structures are captured by learning the representation of the center node along the shortest paths starting from it, and the redundancy between layers are mitigated via initial residual difference connection (IRDC). Then the molecular graph is represented by attentive pooling of all node representations. Compared to standard graph convolution, our chain-aware learning scheme offers a more straightforward feature interaction between distant nodes, thus it is able to capture the information about long-range dependency. We provide extensive empirical analysis on real-world datasets to show the outperformance of the proposed method.

Availability and implementation
The MolPath code is publicly available at https://github.com/Assassinswhh/Molpath.
Doubly-robust and heteroscedasticity-aware sample trimming for causal inference
Authors: Khan S , Ugander J 
Published: October 2024

SUMMARY
A popular method for variance reduction in causal inference is propensity-based trimming, the practice of removing units with extreme propensities from the sample. This practice has theoretical grounding when the data are homoscedastic and the propensity model is parametric (Yang & Ding, 2018; Crump et al., 2009), but in modern settings where heteroscedastic data are analyzed with non-parametric models, existing theory fails to support current practice. In this work, we address this challenge by developing new methods and theory for sample trimming. Our contributions are three-fold: first, we describe novel procedures for selecting which units to trim. Our procedures differ from previous works in that we trim not only units with small propensities, but also units with extreme conditional variances. Second, we give new theoretical guarantees for inference after trimming. In particular, we show how to perform inference on the trimmed sub-population without requiring that our regressions converge at parametric rates. Instead, we make only fourth-root rate assumptions like those in the double machine learning literature. This result applies to conventional propensity-based trimming as well and thus may be of independent interest. Finally, we propose a bootstrap-based method for constructing simultaneously valid confidence intervals for multiple trimmed sub-populations, which are valuable for navigating the trade-off between sample size and variance reduction inherent in trimming. We validate our methods in simulation, on the 2007-2008 National Health and Nutrition Examination Survey, and on a semi-synthetic Medicare dataset and find promising results in all settings.
EV-miRNA associated with environmental air pollution exposures in the MADRES cohort
Authors: Foley Helen Bermudez , Eckel Sandrah P , Yang Tingyu , Vigil Mario , Chen Xinci , Marsit Carmen , Farzan Shohreh F , Bastain Theresa M , Habre Rima , Breton Carrie V 
Published: October 2024

Abstract
Air pollution is a hazardous contaminant, exposure to which has substantial consequences for health during critical periods, such as pregnancy. MicroRNA (miRNA) is an epigenetic mechanism that modulates transcriptome responses to the environment and has been found to change in reaction to air pollution exposure. The data are limited regarding extracellular-vesicle (EV) miRNA variation associated with air pollution exposure during pregnancy and in susceptible populations who may be disproportionately exposed. This study aimed to identify EV-miRNA expression associated with ambient, residential exposure to PM2.5, PM10, NO2, O3 and with traffic-related NOx in 461 participants of the MADRES cohort, a low income, predominantly Hispanic pregnancy cohort based in Los Angeles, CA. This study used residence-based modeled air pollution data as well as Nanostring panels for EVmiRNA extracted with Qiagen exoRNeasy kits to evaluate 483 miRNA in plasma in early and late pregnancy. Average air pollution exposures were considered separately for 1-day, 1-week, and 8-week windows before blood collection in both early and late pregnancy. This study identified 63 and 66 EV-miRNA significantly associated with PM2.5 and PM10, respectively, and 2 miRNA associated with traffic-related NOX (False Discovery Rate-adjusted P-value &lt; .05). Of 103 unique EV-miRNA associated with PM, 92% were associated with lung conditions according to HMDD (Human miRNA Disease Database) evidence. In particular, EV-miRNA previously identified with air pollution exposure also associated with PM2.5 and PM10 in this study were: miR-126, miR-16-5p, miR-187-3p, miR200b-3p, miR486-3p, and miR-582-3p. There were no significant differences in average exposures in early vs late pregnancy. Significant EV-miRNAs were only identified in late pregnancy with an 8-week exposure window, suggesting a vulnerable timeframe of exposure, rather than an acute response. These results describe a wide array of EV-miRNA for which expression is affected by PM exposure and may be in part mediating the biological response to ambient air pollution, with potential for health implications in pregnant women and their children.
Campylobacter fetus Plasmid Diversity: Comparative Analysis of Fully Sequenced Plasmids and Proposed Classification Scheme
Authors: Pena-Fernández Nerea , van der Graaf-van Bloois Linda , Duim Birgitta , Zomer Aldert , Wagenaar Jaap A , Ocejo Medelin , Lavín Jose Luís , Collantes-Fernández Esther , Hurtado Ana , Aduriz Gorka 
Published: October 2024

Abstract
Campylobacter fetus is an animal pathogen that contains 2 mammal-associated subspecies: Campylobacter fetus subsp. fetus (Cff) and Campylobacter fetus subsp. venerealis (Cfv) including its biovar intermedius that exhibit different biochemical traits and differences in pathogenicity. Although plasmids are important in the horizontal transfer of antimicrobial resistance genes and virulence factors, C. fetus plasmids are understudied. Here, the closed sequences of 12 plasmids from Spanish C. fetus isolates were compared with the publicly available DNA sequences of C. fetus plasmids and other members of the Campylobacterales order. Sizes of C. fetus plasmids from Spanish isolates ranged between 4 and 50 kb and most of them (10/12) were potentially conjugative. Comparative analysis of the plasmids’ gene content revealed a close genetic relationship between the plasmids of C. fetus isolated in Spain and those from other geographical regions, while being clearly distinct from plasmids of other Campylobacter species. Furthermore, C. fetus plasmids were grouped into two main clusters regardless of their geographic location or lineage. The distribution pattern of relaxase, replicase, and single-stranded DNA binding SSB protein encoding genes showed a clustering comparable to that resulting from plasmid whole gene content analysis, suggesting its potential use for the classification of C. fetus plasmids. Most of the larger plasmids harbored mobile genetic elements. These results can help to better understand the evolutionary dynamics and pathogenic implications of C. fetus plasmids.
The Evolution of Extreme Genetic Variability in a Parasite-Resistance Complex
Authors: Naser-Khdour Suha , Scheuber Fabian , Fields Peter D , Ebert Dieter 
Published: October 2024

Abstract
Genomic regions that play a role in parasite defense are often found to be highly variable, with the major histocompatibility complex serving as an iconic example. Single nucleotide polymorphisms may represent only a small portion of this variability, with Indel polymorphisms and copy number variation further contributing. In extreme cases, haplotypes may no longer be recognized as orthologous. Understanding the evolution of such highly divergent regions is challenging because the most extreme variation is not visible using reference-assisted genomic approaches. Here we analyze the case of the Pasteuria Resistance Complex in the crustacean Daphnia magna, a defense complex in the host against the common and virulent bacterium Pasteuria ramosa. Two haplotypes of this region have been previously described, with parts of it being nonhomologous, and the region has been shown to be under balancing selection. Using pan-genome analysis and tree reconciliation methods to explore the evolution of the Pasteuria Resistance Complex and its characteristics within and between species of Daphnia and other Cladoceran species, our analysis revealed a remarkable diversity in this region even among host species, with many nonhomologous hyper-divergent haplotypes. The Pasteuria Resistance Complex is characterized by extensive duplication and losses of Fucosyltransferase (FuT) and Galactosyltransferase (GalT) genes that are believed to play a role in parasite defense. The Pasteuria Resistance Complex region can be traced back to common ancestors over 250 million years. The unique combination of an ancient resistance complex and a dynamic, hyper-divergent genomic environment presents a fascinating opportunity to investigate the role of such regions in the evolution and long-term maintenance of resistance polymorphisms. Our findings offer valuable insights into the evolutionary forces shaping disease resistance and adaptation, not only in the genus Daphnia, but potentially across the entire Cladocera class.
Objects in Relations: Competing Visions of International Order at the Nexus of Human Rights and Development
Authors: Pantzerhielm Laura 
Published: October 2024

Abstract
How is international order constructed and maintained, disrupted, and struggled about? In this article, I throw new light on these perennial questions of IR scholarship by turning attention to how expert knowledge and the objects it brings forth invite different ways of ordering. Theoretically, I develop a relational ontology of objects through a rereading of Foucauldian archeology and work in political ontology. My empirical story examines two objects of expertise that relate the more encompassing and elusive governance objects “human rights” and “development” in sharply contrasting ways. Born out of postcolonial legal discourse at the United Nations and the political project of “Third World” solidarity, the notion of a human right to development posits development as a human right and makes sense of its realization within an anti-colonial imaginary that politicizes international institutions and interstate relations. In contrast, the “human rights-based approach” that has lately been embraced as a normative methodology by United Nations development agencies evokes a hierarchical vision that privileges norms and knowledge that are seen as international, global, or universal, while seeking to improve and remold actors and practices in developing countries in their image. Despite their seemingly technical nature and international organizations’ well-documented tendency to downplay their value judgments, objects of expertise are thus entangled in and co-constitute different, potentially conflicting visions of international order.
Maribavir use in pediatric immunocompromised hosts: A case series to talk about real-world experience
Authors: Doshi Shreya , Dassner Aimee , Hanisch Benjamin 
Published: October 2024

Abstract

Background
Cytomegalovirus (CMV) is a common infection affecting pediatric immunocompromised hosts. The treatment of CMV in solid organ (SOT) or hematopoietic stem cell transplant (HSCT) patients is challenged by the toxicities associated with antiviral therapies (myelosuppression with valganciclovir, ganciclovir and cidofovir; nephrotoxicity with foscarnet and cidofovir) and the prevalence of resistant/refractory CMV. Maribavir, a novel benzimidazole, competitively inhibits CMV UL97 protein kinase to inhibit DNA synthesis and block nuclear exit of viral particles from CMV-infected cells. It is FDA approved for use in patients at least 12 years of age and weighing at least 35 kg. The use of maribavir in pediatric patients is of interest due to its availability as an oral dosage formulation and improved side effect profile. To date, there are no pediatric case series or studies describing the use of maribavir for CMV treatment.

Methods
This study is a retrospective case series compiling the findings the first pediatric patients at Children’s National Hospital, DC that received maribavir. We included children who received maribavir from 01/2017 – 10/2023. Patients were included if they were on maribavir monotherapy, or combination therapy with additional anti-CMV agent(s). The medical records were reviewed for indication of medication use, viral response to therapy and side effects. Side-effects review specifically evaluated for increased LFTs, increased serum creatinine, and decreased absolute neutrophil count or factors that may contribute to early discontinuation of maribavir.

Results (table)
Maribavir was used in three male patients with varied conditions – including solid organ transplant (SOT), hematopoietic stem cell transplant (HSCT) and Severe Combined Immunodeficiency (SCID) s/p HSCT. Two cases had signs of CMV disease, and one had CMV viremia. All cases included documented CMV resistance (n=2) or refractory CMV (n=1) and had previously been receiving at least one antiviral with CMV activity for at least 14 days and had increasing CMV DNA-emia in the blood. None of the patients had side effects such as nephrotoxicity, liver toxicity or myelosuppression that aggravated after starting maribavir. Dosing of 400mg BID (range 12mg/kg/day to 55mg/kg/day) was used. Once started, maribavir was continued until CMV quantitative levels were undetectable for two weeks. Clearance of CMV and was achieved in all the patients on maribavir or combination of maribavir with other drugs (n=1). Duration of maribavir treatment ranged from 4.2 to 6.2 weeks.

Conclusion
This is the first case series describing use of maribavir in a pediatric population. In this small cohort maribavir is effective and well tolerated. Further studies are needed to better CMV care in children with immunocompromised conditions.
Unique encounter of a branchial cleft cyst compressing the great auricular nerve in an adult: a case report
Authors: AlHabil Yazan , Dola Qasem N , Saadeddin Liza , Sharabati Haneen 
Published: October 2024

Abstract
Branchial cleft cysts, arising from developmental anomalies of the branchial apparatus, represent a rare entity in adult populations. This case report presents a unique instance of a 32-year-old female with a second branchial cleft cyst prominently involving the great auricular nerve, an undocumented finding in the existing literature. The patient initially presented with progressive left-sided neck swelling, accompanied by localized pain radiating to the auricle and headaches, without systemic symptoms. Diagnostic imaging confirmed a cystic mass adjacent to vital neck structures, necessitating surgical intervention. Histopathological analysis post-excision confirmed typical features of a benign branchial cyst. The postoperative course was uneventful, with complete resolution of symptoms upon follow-up. This case capitalizes the diagnostic challenges and therapeutic considerations in managing branchial cleft cysts, particularly highlighting the exceptional involvement of the great auricular nerve. Further research is warranted to elucidate the pathogenesis and optimal management strategies for such atypical presentations.
Dialysis-associated steal syndrome as a rare complication of arteriovenous fistula angioplasty
Authors: Lim Fang Nian Joanne , Ng Zhi Peng Nick 
Published: October 2024

Abstract
The angioplasty of arteriovenous fistulas (AVF) has become indispensable in preserving haemodialysis access. Though well-known complications, such as pseudoaneurysm formation and rupture, can occur, the incidence of severe dialysis-associated steal syndrome (DASS) following AVF angioplasty is low. We describe a patient with limited dialysis options who developed significant DASS following angioplasty of his AVF. After excluding flow-limiting causes of DASS, the patient underwent a successful Revision Using Distal Inflow procedure, redirecting blood flow to his distal arm. Subsequently, all ischaemic symptoms resolved. While effective surgical options are available for the management of DASS, preventive measures such as proper angioplasty balloon sizing remain key.
The safety and efficacy of antibiotic-impregnated envelopes in neuromodulation device implantation: a systematic review and meta-analysis protocol
Authors: Daniel Jeremiah Oluwatomi Itodo , Igoli Joanne , Isiakpona Chiwendu , Fenny Benjamin , Osei-Bonsu Joshua , Alemede Peace , Olukoya Olatomiwa , Osunronbi Temidayo 
Published: October 2024

Abstract
Introduction: The implantation of neuromodulation devices is an effective treatment option for neurological conditions, including movement disorders. However, there are associated risks of infection and reoperation. Antibiotic-impregnated envelopes may mitigate these risks, as demonstrated in cardiology, but their safety and efficacy in neuromodulation remain unexplored. This study seeks to evaluate the efficacy of antibiotic-impregnated envelopes in reducing infection and reoperation rates in neuromodulation surgeries, offering recommendations to enhance safety and cost-effectiveness in neuromodulation therapies. Methods and Analysis: Following PRISMA and SWiM guidelines, we will conduct an exhaustive search across major databases, including Medline, Embase, Scopus and the Cochrane Library, to identify all original research articles that investigate the efficacy of antibacterial envelopes for neuromodulation implants and report outcomes with the use of these envelopes. Exclusion criteria include reviews, meta-analyses, case studies, letters to the editor and abstract-only articles. Primary outcomes will include infection rates post-implantation, while secondary outcomes will encompass safety metrics such as complications, reoperation rates and cost-effectiveness. Comprehensive data extraction will capture the study design, participant demographics, specific neuromodulation procedures and detailed outcome measures. Study findings will provide critical insights into the effectiveness of antibiotic-impregnated envelopes in improving patient outcomes in neuromodulation procedures. PROSPERO Registration Number: CRD42024549200: available via https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42024549200
Geospatial Analysis of Malaria Burden in Kagera Region, Northwestern Tanzania Using Health Facility and Community Survey Data
Authors: Petro Daniel A , Shaban Nyimvua , Aaron Sijenunu , Chacky Frank , Lazaro Samuel , Boni Maciej F , Ishengoma Deus S 
Published: October 2024

Abstract

Background
Malaria transmission in Tanzania has declined significantly over the last 2 decades due to scaled-up control interventions. However, recent confirmation of artemisinin partial resistance (ART-R) in Kagera region in northwest Tanzania threatens the ongoing efforts to eliminate malaria in the country. This study was conducted according to the World Health Organization recommendation to generate evidence of malaria burden in areas with confirmed ART-R as the first step before developing a response strategy to the resistance.

Methods
We assessed the local burden of malaria in Kagera region by geospatial analysis, using data collected retrospectively from health facilities and community surveys from 2015 to 2023 to identify malaria hot spots.

Results
From 2017 to 2023, a total of 8 124 363 suspected malaria cases were reported by health facilities, and 2 983 717 (36.7% [95% range across wards, 22.7%–50.7%]) tested positive by rapid diagnostic tests. Test positivity rates were similar among patients aged &lt;5 years (33.1% [95% range, 19.7%–46.5%]) and those aged ≥5 years (33.7% [21.0%–46.5%]). The malaria prevalence was 10.0% (95% range across wards, 5.1%–14.9% [n = 84 999 of 853 761]) in pregnant women and 26.1% (11.7%–40.6% [n = 3409 of 13 065]) in schoolchildren. Despite high temporal variations, we identified hot spots and cold spots, including persistently high burden in 69 of 192 wards (35.9%).

Conclusions
The malaria burden in Kagera exhibited high temporal and spatial heterogeneity, with schoolchildren showing the highest prevalence. This demographic pattern underlines the need for targeted interventions and provides evidence for developing an ART-R response for the region.