bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outpatient Treatment With Gabapentin in Women With Severe Acute Pain after Cesarean Delivery is Ineffective: A Randomized, Double-blind, Placebo-controlled Trial
Authors: Fowler C. , Chu A.W. , Guo N. , Ansari J.R. , Shafer S.L. , Flood P.D. 
Published: November 2023

(Anesth Analg. 2023;136:1122–1132)
Cesarean delivery (CD) is a common major surgery but frequently recoveries are uncomplicated. However, in some cases high pain levels during recovery last longer than expected, leading to continued postpartum opioid use. This circumstance is rare, but serious in those who experience it. One common method to reduce opioid use in this population is the prescription of gabapentin, though questions have been raised about its effectiveness. This study was designed to assess the effectiveness of gabapentin in stopping opioid use, reducing pain, and aiding in functional recovery for women who have continued pain after CD.
Improved outcomes of kidney after liver transplantation after the implementation of the safety net policy
Authors: Attieh Rose Mary , Ibrahim Ramez M. , Ghali Peter , Keaveny Andrew , Croome Kristopher , Hodge David , White Launia , Wadei Hani M. 
Published: November 2023

The number of kidney after liver transplants (KALT) increased after the implementation of the United Network of Organ Sharing (UNOS) safety net policy, but the effects of the policy on KALT outcomes remain unknown. Using the UNOS database, we identified KALT between 60 and 365 days from liver transplant from January 1, 2010, to December 31, 2020. The main outcome was 1- and 3-year patient, liver, and kidney graft survival. Secondary outcomes included 6-month and 1-year acute rejection (AR) of liver and kidney, and 1-year kidney allograft function. Of the 256 KALT, 90 were pre-policy and 166 post-policy. Compared to pre-policy, post-policy 1- and 3-year liver graft survival was higher (54% and 54% vs. 86% and 81%, respectively, p<0.001), while 1- and 3-year kidney graft survival (99% and 75% vs. 92% and 79%, respectively, p=0.19), and 1- and 3-year patient survival (99% and 99% vs. 95% and 89%, respectively, p=0.11) were not significantly different. Subgroup analysis revealed similar trends in patients with and without renal failure at liver transplant. Liver AR at 6 months was lower post-policy (6.3% vs. 18.3%, p=0.006) but was similar (10.5% vs. 13%, p=0.63) at 1 year. Kidney AR was unchanged post-policy at 6 months and 1 year. Creatinine at 1 year did not differ post-policy versus pre-policy (1.4 vs. 1.3 mg/dL, p=0.07) despite a higher proportion of deceased donors, higher Kidney Donor Profile Index, and longer kidney cold ischemia time post-policy (p<0.05 for all). This 3-year follow-up after the 2017 UNOS policy revision demonstrated that the safety net implementation has resulted in improved liver outcomes for patients who underwent KALT with no increased AR of the liver or the kidney allografts.
Isaacs syndrome with LGI1 and CASPR2 antibodies after HPV vaccination: A case report
Authors: Yang Bufan , Wei Wei , Duan Jingfeng , Xiao Pei , Jing Yu , Tang Yufeng 
Published: November 2023

Rationale:
Isaacs syndrome is peripheral nerve hyperexcitability characterized by spontaneous muscle twitching and rigidity and is often associated with antibodies to CASPR2 (contactin-associated protein-like 2) and LGI1 (leucine-rich glioma-inactivated 1). But it is a rare Isaacs syndrome with LGI1 and CASPR2 antibodies after human papilloma virus (HPV) vaccination.

Patient concerns:
The patient presented with limb pain, muscle twitching, numbness in the extremities and around the mouth, and hand rash after the second dose of HPV vaccine.

Diagnoses:
Laboratory tests indicated positive for LGI1 antibodies, CASPR2 antibodies, anti-phosphatidylserine/prothrombin antibodies and anti-sulfatide antibodies, TPO and ATG, IgG E. The patient post-M-wave discharges were seen on F-wave examination of the posterior tibial nerve in both lower limbs. We diagnosis the patient with Isaacs syndrome.

Interventions:
Treatment with the intravenous immunoglobulin (IVIG) treatment, after 5 days of IVIG therapy (0.4 mg/kg/day), the rash on the hand disappeared, the pain was relieved, the sleep improved.

Outcomes:
After 3 Courses of treatment, the clinical manifestations of the nervous system disappeared and negative responsibility antibodies profile.

Lessons:
This case report suggests a possible adverse reaction to HPV vaccination, which could be treated by attempting several periods of IVIG therapy. The underlying immune mechanisms need to be studied with further extensive data.
Investigating the Relationship Between COVID-19 and Celiac Disease. A Dual Research Approach
Authors: Tiberti Claudio , Bonamico Margherita , Nenna Raffaella , Petrarca Laura , Trovato Chiara Maria , Pietropaoli Nicoletta , Fassino Valeria , Midulla Fabio , Lenzi Andrea , Oliva Salvatore , Montuori Monica 
Published: November 2023

Background:
Most evidence on the coronavirus disease 2019 (COVID-19) pandemic, has been obtained from web- or telephone-based surveys. In particular, few laboratory data, often incomplete, have been reported on the frequency of COVID-19-related serology at celiac disease (CD) diagnosis or on the effects of COVID-19 on the development of CD-specific autoimmunity.

Objectives:
The objective of this retrospective cross-sectional case/control study was to: (1) evaluate the frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in 78 children and adolescents at CD diagnosis (CD, 44 females, median age 7.4 years); (2) evaluate the frequency of IgA-anti-transglutaminase antibodies (IgA-tTGAbs) in 97 nonceliac patients (50 females, median age 9.0 years) who contracted SARS-CoV-2 infection during the pandemic (February–April 2021). As a control (CTRL) group, we analyzed 141 healthy subjects (79 females, median age 9.8 years) enrolled during the pandemic.

Methods:
SARS-CoV-2 IgM- and IgG-antibodies were detected by chemiluminescent microparticle immunoassays. IgA-tTGAbs were detected by a fluid-phase radioimmunoassay.

Results:
Six out of 78 (7.7%) CD patients tested positive for SARS-CoV-2Abs, with a frequency not significantly different from CTRL subjects (9.2%). None of the 97 nonceliac COVID-19 patients tested positive for IgA-tTG antibodies.

Conclusion:
These 2 distinct research approaches showed (1) similar frequencies of SARS-CoV-2 immunoreactivities in CD patients and CTRL subjects and, (2) no ability of SARS-CoV-2 to induce a CD-specific immune response, at least in the 3–4 months following SARS-CoV-2 infection.
A Rare Clinical Presentation With a Difficult Imaging Diagnosis of an Intra-articular Clear Cell Sarcoma of the Knee
Authors: Kawasaki Tomonori , Ichikawa Jiro , Imada Hiroki , Onohara Kojiro , Torigoe Tomoaki 
Published: November 2023

Abstract
Clear cell sarcoma, a highly aggressive cell sarcoma with melanotic differentiation, typically occurs in the tendon and aponeuroses of the lower extremities and rarely develops in the intra-articular region. Herein, we present an extremely rare case of clear cell sarcoma originating from the intra-articular knee and suspected as benign tumors due to the benign-looking findings on MRI and PET/CT. The image results in our case were completely consistent with a tenosynovial giant cell tumor, resulting in the misdiagnosis. For differential diagnosis, especially malignant melanoma, histopathology, including IHC and FISH, was indispensable.
Antibiotic Utilisation Patterns in Tanzania: A Retrospective Longitudinal Study Comparing Pre- and Post-COVID-19 Pandemic Using Tanzania Medicines and Medical Devices Authority Data
Authors: Sangeda Raphael Z. , William Sahani M. , Masatu Faustine Cassian , Bitegeko Adonis , Mwalwisi Yonah Hebron , Nkiligi Emmanuel Alphonse , Horumpende Pius Gerald , Fimbo Adam M. 
Published: November 2023

SynopsisBackgroundAntimicrobial resistance (AMR) is a growing public health concern globally, and misuse of antibiotics is a major contributor.ObjectiveThis study investigated antibiotic utilisation patterns before and after the COVID-19 pandemic in Tanzania using data from the Tanzania Medicines and Medical Devices Authority (TMDA).MethodsThis retrospective longitudinal study analysed secondary data. The study compared antibiotics consumption in defined daily doses (DDD) per 1000 inhabitants per day (DID) in two distinct eras: 2018-2019 as the pre-COVID-19 era and 2020-2021 as the post-COVID-19 era. Data was reorganised using Microsoft Power BI, and statistical analysis was conducted using SPSS software.ResultsThe study analysed 10,614 records and found an overall increase in antibiotics consumption from 2018 to 2021. When we divided the consumption of antibiotics into a pre- and post-COVID time period, with the pre-COVID period being 2018 and 2019 and the post-COVID period being 2020 and 2021, we found that the consumption was 61.24 DID in the post-COVID era and 50.32 DID in the pre-COVID era. Levofloxacin had the highest percentage increase in use, with a 700% increase in DID after the pandemic. Azithromycin had a 163.79% increase, while cefotaxime had a 600% increase. In contrast, some antibiotics exhibited a decrease in usage after the pandemic, such as nalidixic acid, which had a 100% decrease, and cefpodoxime, 66.67% decrease.ConclusionThe increase in antibiotic consumption during the COVID-19 pandemic highlights the importance of implementing effective antimicrobial stewardship strategies to prevent AMR, especially during pandemics.
DIGEST: An online tool for designing of multiple reaction monitoring assays
Authors: Gautam Prutyay , Singh Praveen , Mrinal  , Bhaskar Akash , Sacher Sukriti , Dagar Yashesh , Basak Trayambak , Sengupta Shantanu , Ray Arjun 
Published: November 2023

ABSTRACTTargeted proteomics using multiple reaction monitoring (MRM) assays enables fast and sensitive detection of a preselected set of target peptides. This technique utilizes the specificity of precursors to product transitions for quantitative analysis of multiple proteins in a single sample. The success of an MRM experiment depends on the selection of transitions however, given the existing resources, accurately predicting signal intensity of peptides and their fragmentation patterns ab initio is challenging task. We present an alternative for rapid design of MRM transitions for proteomics research: DIGEST. Our method predicts the b and y ions with +1 and +2 charge produced in a collision cell of a mass spectrometer from peptides of multiple proteotypically digested proteins. Additionally, by using the existing knowledge of the fundamental rules for designing transitions, the tool provides optimal MRM transitions, negating the need to undertake prior “discovery” MS studies. We demonstrate that our algorithm is directed toward the selection of MRM precursor and product-ions pairs, and can avoid the pitfalls of interference due to cross-contamination of samples by selecting ion combinations that uniquely map to target peptides. Comparison with SRMAtlas showed that DIGEST successfully predicted the peptide and production pairs in the majority of cases. We believe that DIGEST will facilitate rapid design of MRM assays with increased specificity, reducing the overall time required to design an MRM assay for routine mass-spectrometry. DIGEST is available as a web-based tool athttps://digest.raylab.iiitd.edu.in/
Do deleterious mutations promote the evolution of recombination suppression between X and Y chromosomes?
Authors: Olito Colin , Charlesworth Brian 
Published: November 2023

AbstractAn interesting new model has recently been proposed for the evolution of suppressed recombination between newly evolving X and Y chromosomes, where males are heterozygous for a locus determining sex and females are homozygous (the same principles apply to systems with female heterogamety, with the role of the two sexes reversed). The model appeals to the selective advantage that accrues to a recombination suppressor (e.g., an inversion), which arises on a male-determining haplotype that carries a smaller number of deleterious mutations than average and remains completely associated with the sex determining locus. The underlying logic of the model rests on the idea that, because such an inversion cannot become homozygous, it is “sheltered” from selection against any deleterious recessive mutations it may carry, in contrast to an autosomal inversion. It has been claimed that computer simulations of this process show that the probability that a new inversion becomes fixed within the population of Y chromosomes is substantially higher than expected under selective neutrality, and higher than that for a comparable autosomal inversion. However, analytical population genetic models of some special cases cast doubt on the magnitude of the selective advantage claimed for Y-linked inversions under this process, demanding re-evaluation of the simulation results. The published estimates of fixation probabilities of Y-linked inversions were in fact calculated after excluding inversions that were lost in the first 20 generations. This generates a substantial bias towards high fixation probabilities and obscures comparisons with neutrality. If all simulation runs are included, most parameter sets yield estimates of fixation probabilities that are close to neutral expectation, unless deleterious mutations are close to being completely recessive. The proposed sheltering mechanism is unlikely to provide a robust selective advantage to inversions suppressing recombination between evolving X and Y (or Z and W) chromosomes.
Escaping herbivory through chemical novelty? Field performance and herbivore attack in the cardenolide-producing crucifer plantErysimum cheiranthoides
Authors: Wang Kunqi , van Bergen Erik , Züst Tobias 
Published: November 2023

Abstract1.Plants in the Brassicaceae produce glucosinolates as potent defences against generalist herbivores, but many specialists have evolved the ability to tolerate or even deactivate these compounds. As a possible co-evolutionary response to attack by specialists, plants in the genusErysimumgained the ability to produce cardenolide defences in addition to glucosinolates.2.We grew the dually defendedE. cheiranthoidesand the glucosinolate-defendedBrassica nigraside-by-side in agricultural fields surrounded by other Brassicaceae crops. Over the course of two field seasons, we monitored focal plants to characterise their associated herbivore community, and we quantified herbivore damage and measured plant growth. In the second year, we additionally manipulated herbivore density and plant competition to identify direct and indirect effects on plant fitness.3.Both plant species were attacked by a diverse community of specialist herbivores already present on surrounding Brassicaceae crops. Most herbivores strongly favouredB. nigra, reaching higher densities and causing intense damage that largely suppressed growth of this plant. The same herbivores attackedE. cheiranthoides, but at much lower densities that caused little damage and did not impact plant growth.4.In accordance with differential susceptibilities to herbivores, herbivore removal benefittedB. nigraby reducing damage and increasing plant growth, while it had no positive effect onE. cheiranthoides. In fact, herbivore removal had an indirect negative effect onE. cheiranthoideswhen growing in conspecific pairs, as these plants suffered from increased competition by previously herbivore-suppressedB. nigra.Synthesis: Our results agree with a successful escape ofE. cheiranthoidesfrom specialist herbivory, as even though plants are still attacked when herbivores are abundant, these herbivores cause little damage and cause no reduction in fitness. However, the escape from herbivory has likely come at loss of competitive ability in the absence of herbivores, which would explain why despite its key innovation,E. cheiranthoideshas been unable to gain dominance in any plant community.
Logistic PCA explains differences between genome-scale metabolic models in terms of metabolic pathways
Authors: Zehetner Leopold , Széliová Diana , Kraus Barbara , Hernandez Bort Juan A. , Zanghellini Jürgen 
Published: November 2023

AbstractGenome-scale metabolic models (GSMMs) offer a holistic view of biochemical reaction networks, enabling in-depth analyses of metabolism across species and tissues in multiple conditions. However, comparing GSMMs against each other poses challenges as current dimensionality reduction algorithms or clustering methods lack mechanistic interpretability, and often rely on subjective assumptions. Here, we propose a new approach utilizing logisitic principal component analysis (LPCA) that efficiently clusters GSMMs while singling out mechanistic differences in terms of reactions and pathways that drive the categorization.We applied LPCA to multiple diverse datasets, including GSMMs of 222Escherichia-strains, 343 budding yeasts (Saccharomycotina), 80 human tissues, and 2943Firmicutesstrains. Our findings demonstrate LPCA’s effectiveness in preserving microbial phylogenetic relationships and discerning human tissue-specific metabolic profiles, exhibiting comparable performance to traditional methods like t-distributed stochastic neighborhood embedding (t-SNE) and Jaccard coefficients. Moreover, the subsystems and associated reactions identified by LPCA align with existing knowledge, underscoring its reliability in dissecting GSMMs and uncovering the underlying drivers of separation.Author’s summaryGenome-scale metabolic models (GSMMs) are comprehensive representations of all the biochemical reactions that occur within an organism, enabling insights into cellular processes. Our study introduces logisitic principal component analysis (LPCA) to explore and compare these biochemical networks across different species and tissues only based on the presence or absence of reactions, summarized in a binary matrix. LPCA analyzes these binary matrices of specific biochemical reactions, identifying significant differences and similarities. We applied LPCA to a range of datasets, including bacterial strains, fungi, and human tissues. Our findings demonstrate LPCA’s effectiveness in distinguishing microbial phylogenetic relationships and discerning tissue-specific profiles in humans. LPCA also offers precise information on the biochemical drivers of these differences, contributing to a deeper understanding of metabolic subsystems. This research showcases LPCA as a valuable method for examining the complex interplay of reactions within GSMMs, offering insights that could support further scientific investigation into metabolic processes.
The integration of tactile and proprioceptive signals to achieve haptic object perception
Authors: Dogruoz R. Efe , Shelchkova Natalya S. , Sheets Drew E. , Greenspon Charles M. , Bensmaia Sliman J. 
Published: November 2023

AbstractStereognosis, the sense of the 3-dimensional shape of objects held in hand, requires the integration of somatosensory signals about local features -such as edges and surface curvature- with proprioceptive signals about the conformation of the fingers on the object. However, the mechanism of this integration remains unknown. Here, we investigated the spatial model that is used to integrate information about the global shape of the object with information about its local features at each point of contact. To this end, human observers judged the dissimilarity of pairs of objects that differed in their global shape, their local features, or both. We then compared the dissimilarity ratings when both global shape and local features changed to ratings when only global shape or only local features changed. We tested this with object sets of different levels of complexity, including spheres of different sizes and surface features to more varied shapes and features. For all object sets, we found that ratings when both global shape and local features changed was approximately an additive combination of the ratings when only global shape or only local features changed. For the majority of subjects, a city-block spatial model best explained their responses. Our results suggest that information about global shape is encoded independently from that about local features during interactions with objects. This implies that the neural representations of object shape and local features, though integrated, are separable.
Multicellular magnetotactic bacterial consortia are metabolically differentiated and not clonal
Authors: Schaible George A. , Jay Zackary J. , Cliff John , Schulz Frederik , Gauvin Colin , Goudeau Danielle , Malmstrom Rex R. , Ruff S. Emil , Edgcomb Virginia , Hatzenpichler Roland 
Published: November 2023

AbstractConsortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing eight new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescencein situhybridization (FISH) combined with nano-scale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal non-canonical amino acid tagging (BONCAT) we explored theirin situactivity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.Significance statementThe emergence of multicellular lifeforms represents a pivotal milestone in Earth’s history, ushering in a new era of biological complexity. Because of the relative scarcity of multicellularity in the domainsBacteriaandArchaea, research on the evolution of multicellularity has predominantly focused on eukaryotic model organisms. In this study, we explored the complexity of the only known bacteria without a unicellular stage in their life cycle, consortia of multicellular magnetotactic bacteria (MMB). Genomic and physiological analyses revealed that cells within individual MMB consortia are not clonal and exhibit metabolic differentiation. This implies a higher level of complexity than previously assumed for MMB consortia, prompting a reevaluation of the evolutionary factors that have led to the emergence of multicellularity. Because of their unique biology MMB consortia are ideally suited to become a model system to explore the underpinnings of bacterial multicellularity.