bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensory phenotypes in complex regional pain syndrome and chronic low back pain—indication of common underlying pathomechanisms
Authors: De Schoenmacker Iara , Sirucek Laura , Scheuren Paulina S. , Lütolf Robin , Gorrell Lindsay M. , Brunner Florian , Curt Armin , Rosner Jan , Schweinhardt Petra , Hubli Michèle 
Published: November 2023

Abstract

Introduction:
First-line pain treatment is unsatisfactory in more than 50% of chronic pain patients, likely because of the heterogeneity of mechanisms underlying pain chronification.

Objectives:
This cross-sectional study aimed to better understand pathomechanisms across different chronic pain cohorts, regardless of their diagnoses, by identifying distinct sensory phenotypes through a cluster analysis.

Methods:
We recruited 81 chronic pain patients and 63 age-matched and sex-matched healthy controls (HC). Two distinct chronic pain cohorts were recruited, ie, complex regional pain syndrome (N = 20) and low back pain (N = 61). Quantitative sensory testing (QST) was performed in the most painful body area to investigate somatosensory changes related to clinical pain. Furthermore, QST was conducted in a pain-free area to identify remote sensory alterations, indicating more widespread changes in somatosensory processing.

Results:
Two clusters were identified based on the QST measures in the painful area, which did not represent the 2 distinct pain diagnoses but contained patients from both cohorts. Cluster 1 showed increased pain sensitivities in the painful and control area, indicating central sensitization as a potential pathomechanism. Cluster 2 showed a similar sensory profile as HC in both tested areas. Hence, either QST was not sensitive enough and more objective measures are needed to detect sensitization within the nociceptive neuraxis or cluster 2 may not have pain primarily because of sensitization, but other factors such as psychosocial ones are involved.

Conclusion:
These findings support the notion of shared pathomechanisms irrespective of the pain diagnosis. Conversely, different mechanisms might contribute to the pain of patients with the same diagnosis.
Ex-vivo rectal tissue infection with HIV-1 to assess time to protection following oral preexposure prophylaxis with tenofovir disoproxil/emtricitabine
Authors: Chawki Sylvain , Goldwirt Lauriane , Mouhebb Mayssam El , Gabassi Audrey , Taouk Milad , Bichard Iris , Loze Bénédicte , Amara Ali , Brand Rhonda , Siegel Aaron , McGowan Ian , Costagliola Dominique , Assoumou Lambert , Molina Jean-Michel , Delaugerre Constance ,   the ANRS PREVENIR Study group
Published: November 2023

Objectives:
We wished to assess time to protection from HIV-1 infection following oral tenofovir disoproxil and emtricitabine (TDF/FTC) as preexposure prophylaxis (PrEP), using ex-vivo rectal tissue infections and drug concentration measures in blood and rectal tissue.

Design/Methods:
Participants from the ANRS PREVENIR study (NCT03113123) were offered this sub-study after a 14-day wash-out. We used an ex-vivo model to evaluate rectal tissue HIV-1 susceptibility before and after PrEP, 2 h after two pills or 7 days of a daily pill of TDF/FTC. PrEP efficacy was expressed by the difference (after-before) of 14-day cumulative p24 antigen levels. TFV-DP and FTC-TP levels were measured in rectal tissue and PBMCs and correlated with HIV-1 infection.

Results:
Twelve and 11 men were analyzed in the 2 h–double dose and 7 days–single dose groups, respectively. Cumulative p24 differences after-before PrEP were -144 pg/ml/mg (IQR[−259;−108]) for the 2 h–double dose group (P = 0.0005) and -179 pg/ml/mg (IQR [−253;−86]) for the 7 days–single dose group (P = 0.001), with no differences between groups (P = 0.93). Rectal TFV-DP was below quantification after a double dose, but FTC-TP levels were similar to levels at 7 days. There was a significant correlation between rectal FTC-TP levels and p24 changes after a double dose (R = −0.84; P = 0.0001).

Conclusion:
Oral TDF/FTC provided similar protection against HIV-1 infection of rectal tissue 2 h after a double dose or 7 days of a daily dose. At 2 h, this protection seems driven by high FTC-TP concentrations in rectal tissue. This confirms the importance of combining TDF and FTC to achieve early protection.
Weight loss associated with semaglutide treatment among people with HIV
Authors: Haidar Lara , Crane Heidi M. , Nance Robin M. , Webel Allison , Ruderman Stephanie A. , Whitney Bridget M. , Willig Amanda L. , Napravnik Sonia , Mixson L. Sarah , Leong Christine , Lavu Alekhya , Aboulatta Laila , Dai Mindy , Hahn Andrew , Saag Michael S. , Bamford Laura , Cachay Edward , Kitahata Mari M. , Mayer Kenneth H. , Jacobson Jeffrey , Moore Richard D. , Delaney Joseph A.C. , Drumright Lydia N. , Eltonsy Sherif 
Published: November 2023

Objective:
There is limited real-world evidence about the effectiveness of semaglutide for weight loss among people with HIV (PWH). We aimed to investigate weight change in a US cohort of PWH who initiated semaglutide treatment.

Design:
Observational study using the Centers for AIDS Research Network of Integrated Clinical Systems (CNICS) cohort.

Methods:
We identified adult PWH who initiated semaglutide between 2018 and 2022 and with at least two weight measurements. The primary outcome was within-person bodyweight change in kilograms at 1 year. The secondary outcome was within-person Hemoglobin A1c percentage (HbA1c) change. Both outcomes were estimated using multivariable linear mixed model.

Results:
In total, 222 new users of semaglutide met inclusion criteria. Mean follow-up was 1.1 years. Approximately 75% of new semaglutide users were men, and at baseline, mean age was 53 years [standard deviation (SD): 10], average weight was 108 kg (SD: 23), mean BMI was 35.5 kg/m2, mean HbA1c was 7.7% and 77% had clinically recognized diabetes. At baseline, 97% were on ART and 89% were virally suppressed (viral load < 50 copies/ml). In the adjusted mixed model analysis, treatment with semaglutide was associated with an average weight loss of 6.47 kg at 1 year (95% CI −7.67 to −5.18) and with a reduction in HbA1c of 1.07% at 1 year (95% CI −1.64 to −0.50) among the 157 PWH with a postindex HbA1c value.

Conclusion:
Semaglutide was associated with significant weight loss and HbA1c reduction among PWH, comparable to results of previous studies from the general population.
Correction of Unicoronal Synostosis With Springs: Two Patients With Improved Facial Symmetry
Authors: Bhatti-Søfteland Madiha , Mellgren Jonas , Säljö Karin , Tarnow Peter , Maltese Giovanni , Olsson Robert , Hallén Tobias , Kölby Lars 
Published: November 2023

Objective:
Surgical correction of unicoronal synostosis (UCS) entails extensive cranioplasties which do not address facial scoliosis. This paper presents the first results with springs that motivated the shift from extensive cranioplasties to dynamic techniques for surgical correction of UCS.

Methods:
Two cases of UCS were operated with a linear osteotomy combined with springs. The deviation in facial symmetry (orbital dystopia angle) and skull base angles were measured on pre and postoperative computed tomography scans until 3 years of age.

Results:
The facial scoliosis was corrected. At spring removal, the orbital dystopia angle had gone from a 9.2 to 13.2-degree deviation preoperatively to a 0.5 to 0.9-degree overcorrection compared with the ideal 0-degree deviation. Also, the skull base deviation improved.

Conclusion:
Linear osteotomy combined with springs corrects the facial scoliosis in UCS. These cases indicate that dynamic methods may be beneficial for improving the results of surgical correction of UCS.
A shift in the host web occupancy of dew-drop spiders associated with genetic divergence in the Southwest Pacific
Authors: Elias Noraya U. , Responte Mae A. , Wu Cheng-Yu , Chiu Yi-Fan , Peng Po , Liao Hauchuan , Brown Rafe M. , Su Yong-Chao 
Published: November 2023

ABSTRACTAimWe assessed the population genetic structure of the kleptoparasitic spiderArgyrodes bonadeaacross the Southwestern Pacific islands. Our focus is on assessing the impact of overseas distances and, in particular, the Kerama gap, as potential drivers of genetic differentiation. We found that the spider kleptoparasite’s switch to a specific host species is associated with significant genetic variation at fine scales, whereas the same species adoption of a generalist host strategy has likely facilitated its broad dispersal, colonization, and recent range expansion across the southwestern Pacific, and is associated with a lack of geographically– structured genetic variation in these latter, subsequently-colonized landmasses.LocationSouthwestern Pacific IslandsTaxonArgyrodes bonadeaMethodsWe used mitochondrial Cytochrome Oxidase 1 (CO1) gene sequences, and Restriction Site-associated DNA Sequencing (RAD-seq) for our analyses.ResultsTwo strongly supported lineages, an Amami-Okinawa Lineage (AOL) and an Austral-Asia Lineage (AAL) correspond to two separate clades, roughly divided by the Kerama Gap, in phylogenetic trees estimated here. However, species delimitation led to the interpretation of only a single species present. The AOL exhibits complex, geographically-structured host web spider species specificity, wherein the Amami population utilizesCyrtophora, but AOL samples in Okinawa associates exclusively withNephila—and yet all broadly distributed AAL populations show no evidence of host web spider species specificity.Main conclusionThe population boundary between AOL and AAL likely results from local adaptation to novel hosts—instead of isolation by the Kerama Gap—following long-distance dispersal and range expansion. Our results suggest kleptoparasitic spiders have the capacity to overcome permanent deep-sea barriers and colonize distant landmasses. Whereas peripheral populations (AOL) demonstrate the capacity for specialization to a single host, which may have contributed to genetic differentiation and isolation, the broadly-distributed AAL persists and has successfully expanded its geographical range as a host generalist, which may contribute to ongoing gene flow inferred in this study.
Recombination hotspots inNeurospora crassacontrolled by idiomorphic sequences and meiotic silencing
Authors: Yeadon P. Jane , Bowring Frederick J. , Catcheside David E. A. 
Published: November 2023

AbstractGenes regulating recombination in specific chromosomal intervals ofNeurospora crassawere described in the 1960s but the mechanism is still unknown. For each of therec-1,rec-2andrec-3genes, a single copy of the putative dominant allele, for examplerec-2SLfound in St Lawrence OR74 A wild type, reduces recombination in chromosomal regions specific to that gene. However, when we sequenced the recessive allele,rec-2LG(derived from the Lindegren 1A wild type) we found that a 10 kb region inrec-2SLstrains was replaced by a 2.7 kb unrelated sequence, making the “alleles” idiomorphs. When we introducedsad-1, a mutant lacking the RNA-dependent RNA polymerase that silences unpaired coding regions during meiosis into crosses heterozygousrec-2SL/rec-2LG, it increased recombination, indicating that meiotic silencing of a gene promoting recombination is responsible for dominant suppression of recombination. Consistent with this, mutation ofrec-2LGby RIP (repeat induced mutation) generated an allele with multiple stop codons in the predictedrec-2gene, which does not promote recombination and is recessive torec-2LG.sad-1also relieves suppression of recombination in relevant target regions, in crosses heterozygous forrec-1alleles and in crosses heterozygous forrec-3alleles. We conclude that for all three knownrecgenes, one allele appears dominant only because meiotic silencing prevents the product of the active, “recessive”, allele from stimulating recombination during meiosis. In addition, the proposed amino acid sequence of REC-2 indicates regulation of recombination in Neurospora differs from any currently known mechanism.
MP-GNN: Graph Neural Networks to Identify Moonlighting Proteins
Authors: Zhou Hongliang , Sarkar Rik 
Published: November 2023

ABSTRACTMoonlighting proteins are those proteins that perform more than one distinct function in the body. They are pivotal in various metabolic pathways and disease mechanisms. Identifying moonlighting proteins remains a challenge in Computational Biology. In this work, we propose the first graph neural network based models to identify moonlighting proteins. Our models work on large protein-protein interaction (PPI) networks with sparse labels of moonlighting and non-moonlighting proteins. In addition to PPI network, the models make use of features derived from the amino acid sequences of the proteins.We propose two frameworks: one as graph classification based on the local neighborhood of the query protein; and the other node classification based on the entire graph. These GNN-based methods outperform traditional machine learning methods that have previously been used for moonlighting prediction. The global full network-based model, operating onHomo sapiensdata achieves accuracy of 88.4% and F1 score of 88.8%. The local neighborhood method is more lightweight and can be applied to larger protein sets with multiple species.CCS CONCEPTS• Applied computing → Computational proteomics.
Human brain glycoform co-regulation network and glycan modification alterations in Alzheimer’s disease
Authors: Zhang Qi , Ma Cheng , Chin Lih-Shen , Pan Sheng , Li Lian 
Published: November 2023

AbstractDespite the importance of protein glycosylation to brain health, current knowledge of glycosylated proteoforms or glycoforms in human brain and their alterations in Alzheimer’s disease (AD) is limited. Here, we present a new paradigm of proteome-wide glycoform profiling study of human AD and control brains using intact glycopeptide-based quantitative glycoproteomics coupled with systems biology. Our study identified over 10,000 human brain N-glycoforms from nearly 1200 glycoproteins and uncovered disease signatures of altered glycoforms and glycan modifications, including reduced sialylation and N-glycan branching as well as elevated mannosylation and N-glycan truncation in AD. Network analyses revealed a higher-order organization of brain glycoproteome into networks of co-regulated glycoforms and glycans and discovered glycoform and glycan modules associated with AD clinical phenotype, amyloid-β accumulation, and tau pathology. Our findings provide novel insights and a rich resource of glycoform and glycan changes in AD and pave the way forward for developing glycosylation-based therapies and biomarkers for AD.
Evaluation of gelatin bloom strength on gelatin methacryloyl hydrogel properties
Authors: Zambuto Samantha G. , Kolluru Samyuktha S. , Ferchichi Eya , Rudewick Hannah F. , Fodera Daniella M. , Myers Kristin M. , Zustiak Silviya P. , Oyen Michelle L. 
Published: November 2023

ABSTRACTGelatin methacryloyl (GelMA) hydrogels are widely used for a variety of tissue engineering applications. The properties of gelatin can affect the mechanical properties of gelatin gels; however, the role of gelatin properties such as bloom strength on GelMA hydrogels has not yet been explored. Bloom strength is a food industry standard for describing the quality of gelatin, where higher bloom strength is associated with higher gelatin molecular weight. Here, we evaluate the role of bloom strength on GelMA hydrogel mechanical properties. We determined that both bloom strength of gelatin and weight percent of GelMA influenced both stiffness and viscoelastic ratio; however, only bloom strength affected diffusivity, permeability, and pore size. With this library of GelMA hydrogels of varying properties, we then encapsulated Swan71 trophoblast spheroids in these hydrogel variants to assess how bloom strength affects trophoblast spheroid morphology. Overall, we observed a decreasing trend of spheroid area and Feret diameter as bloom strength increased. In identifying clear relationships between bloom strength, hydrogel mechanical properties, and trophoblast spheroid morphology, we demonstrate that bloom strength should considered when designing tissue engineered constructs.
SANTA FE OXA: Self-assembled oxaliplatin nanomicelle for enhanced cascade cancer chemotherapy via self-sensitized ferroptosis
Authors: Shi Jianbin , Ma Wenjing , Zheng Shunzhe , Xia Fengli , Liu Xinying , Kikkawa Ayumi , Tanaka Kaho , Kamei Ken-ichiro , Tian Chutong 
Published: November 2023

AbstractThe clinical utility of chemotherapy is often compromised by its limited efficacy and significant side effects. Addressing these concerns, we develop a self-assembled nanomicelle, namely SANTA FE OXA, which is composed of hyaluronic acid (HA) conjugated with ferrocene methanol (FC-OH), oxaliplatin prodrug (OXA(□)) and glycol-coupled linoleic acid (EG-LA). Targeted delivery is achieved as HA binds to the CD44 receptors that are overexpressed on tumor cells, facilitating drug uptake. Once internalized, hyaluronidase (HAase) catalyzes the digestions of the SANTA FE OXA, releasing FC and reducing OXA(□) into an active form. Active OXA induces DNA damage, while simultaneously promoting intracellular hydrogen peroxide levels via cascade reactions. In parallel, FC disrupts the redox balance within tumor cells, inducing ferroptosis. The synergistic combination of cascade chemotherapy and self-sensitized ferroptosis therapy has demonstrated remarkable anti-cancer efficacy in bothin vitroandin vivomodels. Moreover, this SANTA FE OXA significantly mitigates the systemic toxicity commonly associated with platinum-based chemotherapeutics. Our findings suggest a compelling advancement in nanomedicine for enhanced cascade cancer therapy.
Analysis of Sequences of Bases of Human DNA Using the Square Wave Method (SWM)
Authors: Skliar Osvaldo , Gapper Sherry , Monge Ricardo E. 
Published: November 2023

AbstractA description is provided of how the Square Wave Method (SWM) can be applied to analyze sequences of bases of human DNA. The results obtained are displayed using the Square Wave Transform (SWT), an SWM tool. It is hypothesized that the results of this analysis can be of interest, in certain cases, to understand the functional role of some of those sequences. Preliminary data which make this hypothesis plausible are presented.
Dynamic functional connectivity encodes generalizable representations of emotional arousal across individuals and situational contexts
Authors: Ke Jin , Song Hayoung , Bai Zihan , Rosenberg Monica D. , Leong Yuan Chang 
Published: November 2023

AbstractHuman affective experience varies along the dimensions of valence (positivity or negativity) and arousal (high or low activation). It remains unclear how these dimensions are encoded in the brain and if the representations are shared across different individuals and diverse situational contexts. Here we utilized two publicly available functional MRI datasets of participants watching movies to build predictive models of moment-to-moment valence and arousal from dynamic functional brain connectivity. We tested the models both within and across datasets and identified a generalizable arousal representation characterized by the interaction between multiple large-scale functional networks. The arousal representation generalized to two additional movie-watching datasets. Predictions based on multivariate patterns of activation underperformed connectome-based predictions and did not generalize. In contrast, we found no evidence of a generalizable valence representation. Taken together, our findings reveal a generalizable representation of arousal encoded in patterns of dynamic functional connectivity, revealing an underlying similarity in how arousal is encoded across individuals and situational contexts.
A Large Field-of-view, Single-cell-resolution Two- and Three-Photon Microscope for Deep Imaging
Authors: Mok Aaron T. , Wang Tianyu , Zhao Shitong , Kolkman Kristine E. , Wu Danni , Ouzounov Dimitre G , Seo Changwoo , Wu Chunyan , Fetcho Joseph R. , Xu Chris 
Published: November 2023

AbstractIn vivo imaging of large-scale neuron activity plays a pivotal role in unraveling the function of the brain’s network. Multiphoton microscopy, a powerful tool for deep-tissue imaging, has received sustained interest in advancing its speed, field of view and imaging depth. However, to avoid thermal damage in scattering biological tissue, field of view decreases exponentially as imaging depth increases. We present a suite of innovations to overcome constraints on the field of view in three-photon microscopy and to perform deep imaging that is inaccessible to two-photon microscopy. These innovations enable us to image neuronal activities in a ∼3.5-mm diameter field-of-view at 4 Hz with single-cell resolution and in the deepest cortical layer of mouse brains. We further demonstrate simultaneous large field-of-view two-photon and three-photon imaging, subcortical imaging in the mouse brain, and whole-brain imaging in adult zebrafish. The demonstrated techniques can be integrated into any multiphoton microscope for large-field-of-view and system-level neural circuit research.
Can a flower color ancestral polymorphism transcend speciation?
Authors: Sánchez-Cabrera Mercedes , Narbona Eduardo , Arista Montserrat , Ortiz Pedro L. , Jiménez-López Francisco J. , Fuller Amelia , Carter Benjamin , Whittall Justen B. 
Published: November 2023

AbstractPolymorphisms are common in nature, but they are rarely shared among closely related species. They could originate through convergence, ancestral polymorphism, or introgression. Although shared neutral genomic variation is commonplace, very few examples of shared functional traits exist. The blue-orange petal color polymorphisms in two closely related species,Lysimachia monelliandL. arvensiswere investigated with UV-vis reflectance spectra, flavonoid biochemistry, and transcriptome comparisons followed by climate niche analysis. The similarities in reflectance spectra, biochemistry, and transcriptomes suggest a single shift from blue-to-orange shared by both lineages is possible. Transcriptome comparisons reveal two orange-specific genes are directly involved in both blue-orange color polymorphisms:DFR-2specificity redirects flux from the malvidin to the pelargonidin whileBZ1-2stabilizes the pelargonidin with glucose, producing the orange pelargonidin 3-glucoside. The climate niches for each color morph are the same between the two species for three temperature characteristics but differ for four precipitation variables. We suggest that this persistent flower color polymorphism may represent an ancestrally polymorphic trait that has transcended speciation with some unique ecological effects.