bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of diabetes mellitus on HIV virologic control: results of the MACS/WIHS combined cohort study
Authors: Mann Sarah C. , Tong Weiqun , Abraham Alison G. , Palella Frank , Sharma Anjali , Tien Phyllis C. , Fischl Margaret A. , McFarlane Samy I. , Lahiri Cecile D. , Koletar Susan , Merenstein Daniel , Floris-Moore Michelle , Lake Jordan E. , Daubert Elizabeth , Hickman Aubri , Brown Todd T. , Castillo-Mancilla Jose 
Published: July 2024

Objective:
Diabetes mellitus (DM) is associated with lower antiretroviral (ART) drug exposure among persons with HIV (PWH) compared to PWH without DM. The association between DM and virologic control in PWH, however, remains unknown.

Methods:
We included participants in the Multicenter AIDS Cohort Study/Women's Interagency HIV Study Combined Cohort Study (MWCCS) who had initiated ART between 1999 and 2020 and had a suppressed HIV viral load (≤200 copies/ml) within 1 year of ART initiation. We compared the frequency of incident HIV viremia (HIV-1 RNA >200 copies/ml) between adult PWH with and without DM. Poisson regression was used to examine the rate of incident viremia based on the diagnosis of DM among PWH. DM was defined as two consecutive fasting glucose measurements ≥126 mg/dl, use of antidiabetic medications, preexisting DM diagnosis, or a confirmed HbA1c >6.5%.

Results:
1061 women (112 with DM, 949 without DM) and 633 men (41 with DM, and 592 without DM) were included in the analysis. The relative rate (RR) of incident HIV viremia for women with HIV and DM was lower when compared to women without DM (0.85 [95% CI: 0.72–0.99]; P = 0.04). The RR of incident viremia for women with uncontrolled DM (HbA1c > 7.5%) was higher when compared to women with controlled DM (HbA1c < 7.5%) (1.46 [95% CI: 1.03–2.07]; P = 0.03). In contrast, the RR of incident viremia for men with HIV and DM was not statistically different compared to men without DM (1.2 [95% CI: 0.96–1.50]; P = 0.12). The results were stratified by adherence levels (100%, 95–99%, and <95% based on self-report).

Conclusions:
Women with DM who are highly adherent to ART (100% self-reported adherence) have a lower risk of viremia compared to women with HIV without DM. However, women with poorly controlled DM were at higher risk of HIV viremia than women with controlled DM. Further research is necessary to understand the impact of sex, DM, and ART adherence on HIV viremia.
The Vertical Profunda Artery Perforator Flap for Perineal Reconstruction
Authors: Lavie Jennifer L. , Guidry Richard F. , Palines Patrick A. , Dibbs Rami P. , Melancon Devin M. , Womac Daniel J. , Stalder Mark W. 
Published: July 2024

Background
Colorectal cancer is a significant cause of cancer-related death in the United States with abdominoperineal resection (APR) remaining a necessary procedure for many patients. The resultant defects of this radical operation are complex and characterized by significant tissue voids. Pedicled vertical profunda artery perforator flaps (vPAP) can be used to obliterate these defects in patients receiving minimally invasive APR or when the abdominal donor site is unavailable.

Methods
After receiving local institutional review board approval, a single center, retrospective cohort study from January 2020 to December 2021 was performed assessing pedicled vPAP flap reconstruction of APR defects. Age, sex, body mass index, primary diagnosis, comorbidities, concomitant oncologic procedures, radiation, timing, incorporation of gracilis flaps, follow-up, and complications were compared.

Results
Ten patients (70% male) with an average age of 56.2 years and BMI of 27.6 were included in the study. Rectal adenocarcinoma (50%) was the most common indication for APR, followed by rectal squamous cell carcinoma (30%), vulvar squamous cell carcinoma (10%), and Crohn disease (10%). Eighty percent of the patients received radiation, and 70% of reconstructions were delayed after the initial resection. The average length of clinical follow-up was 26.1 months. Concerning major complications, 2 patients were required to return to the operating room due to venous congestion (20%), and 2 patients suffered partial flap failure (20%). Minor complications were perineal dehiscence (50%), abscess requiring percutaneous drainage by interventional radiology (30%), and infection requiring antibiotics (20%). Twenty percent of patients developed fistulas requiring surgical excision. There were no instances of donor site dehiscence, and there was no complete flap loss, indicating successful reconstruction in all included cases.

Conclusions
vPAP flaps are a reliable method to reconstruct perineal defects with less donor-site morbidity than previous reconstructive options. vPAP flaps should be considered in the setting of delayed reconstruction, minimally invasive APRs, and when the abdominal donor site is unavailable.
Discrepancies Between Objective and Subjective Outcomes of and Quality of Life During Molding Helmet Therapy for Cranial Deformities
Authors: Neumeister Anne , Brand Susanne , Koch Franziska , Kubon Sophie , Baumgarten Peter , Senft Christian , Schwarz Falko , Löschner Denise 
Published: July 2024

Positional skull deformities have been on the rise for decades and can be treated with molding helmets in early childhood. Parents often fear later cosmetic stigmatization, but also a reduced quality of life (QoL) during treatment. The aim of this study was to examine therapy results in our patient collection from a new perspective. Cranial vault asymmetry (CVA), cranial vault asymmetry index (CVAI), and cranial index (CI) were compared before and after molding helmet therapy. Correction was defined by a decrease in CVA <3.5 mm and CI <90%. Subjective therapy outcome, side effects and QoL from the parents’ perspective were determined using a questionnaire. There were 25 patients included. Differences between pretherapeutic and posttherapeutic CVA, CVAI, and CI were significant (P<0.01). An objective correction according to the defined values was observed in only 12% of cases. However, 76% of parents stated that their child’s skull shape was normal after therapy. There were 60 side effects reported in 23 cases. The QoL of 21 children was assessed as unimpaired during helmet therapy. Even though complete normalization was rarely observed, the parameters were significantly different after therapy, and subjective reduction in skull deformity was common.
GPS-Net: discovering prognostic pathway modules based on network regularized kernel learning
Authors: Yao Sijie , Li Kaiqiao , Li Tingyi , Yu Xiaoqing , Kuan Pei Fen , Wang Xuefeng 
Published: July 2024

AbstractThe search for prognostic biomarkers capable of predicting patient outcomes, by analyzing gene expression in tissue samples and other molecular profiles, remains largely on single-gene-based or global-gene-search approaches. Gene-centric approaches, while foundational, fail to capture the higher-order dependencies that reflect the activities of co-regulated processes, pathway alterations, and regulatory networks, all of which are crucial in determining the patient outcomes in complex diseases like cancer. Here, we introduce GPS-Net, a computational framework that fills the gap in efficiently identifying prognostic modules by incorporating the holistic pathway structures and the network of gene interactions. By innovatively incorporating advanced multiple kernel learning techniques and network-based regularization, the proposed method not only enhances the accuracy of biomarker and pathway identification but also significantly reduces computational complexity, as demonstrated by extensive simulation studies. Applying GPS-Net, we identified key pathways that are predictive of patient outcomes in a cancer immunotherapy study. Overall, our approach provides a novel framework that renders genome-wide pathway-level prognostic analysis both feasible and scalable, synergizing both mechanism-driven and data-driven for precision genomics.
WheatTaNADPOpromotes spot blotch resistance
Authors: Yuan Meng , Zeng Qingdong , Hua Lei , Wu Jianhui , Zhao Shuqing , Li Mengyu , Ren Xiaopeng , Su Jun , Ren Zhuang , Ma Linfei , Liu Zihan , Wang Kaixuan , Sun Manli , Yan Hongfei , Kang Zhensheng , Han Dejun , Chen Shisheng , Wang Xiaodong 
Published: July 2024

ABSTRACTBipolaris sorokinianais a common soil-borne fungal pathogen that can infect various organs of wheat (Triticum aestivumL.), causing diseases such as spot blotch, common root rot, head blight, and black point. The genetic basis of wheat resistance toB. sorokinianais not yet fully understood. In this study, a natural population of 1,302 global common wheat germplasms was established and inoculated withB. sorokinianaat the seedling stage in a greenhouse. Resistance to spot blotch was assessed, revealing that only about 3.8% of the germplasms exhibited moderate or higher resistance levels. A genome-wide association study (GWAS) using high-density 660K single nucleotide polymorphism (SNP) data identified a region on chromosome 1BL (621.2-674.0 Mb) with 9 SNPs significantly associated (p< 10e-4) with spot blotch resistance, designated asQsb.hebau-1BL. RNA sequencing and qRT-PCR assays showed that the geneTraesCS1B02G410300, encoding nicotinamide-adenine dinucleotide phosphate-binding oxidoreductase (TaNADPO), was significantly induced byB. sorokiniana. Five SNP variations were found in the promoter region ofTaNADPOin wheat lines with or withoutQsb.hebau-1BL. Transient expression ofTaNADPOinNicotiana benthamianaleaves showed a cytoplasmic subcellular localization of the fusion protein with a green fluorescent protein (GFP) tag. Wheat transgenic lines overexpressingTaNADPOexhibited significantly enhanced resistance to spot blotch compared to wildtype plants, with higher accumulation of reactive oxygen species (ROS). The knockout EMS mutant ofTriticum turgidum NADPO(tdnadpo-K2561, Gln125*) showed significantly reduced resistance to spot blotch and lower ROS accumulation compared to wildtype plants. In summary,TaNADPOhas been identified as a crucial gene for resistance toB. sorokiniana, providing valuable insights for developing spot blotch-resistant wheat varieties through molecular breeding techniques.
Agricultural landscapes with high compositional heterogeneity support both forest and farmland birds in Taiwan
Authors: Lin Da-Li , Amano Tatsuya , Fuller Richard A. , Ding Tzung-Su , Maron Martine 
Published: July 2024

AbstractContextPromoting heterogeneous agricultural landscapes could help to reduce the negative impacts of habitat conversion on biota. However, the benefits of landscape heterogeneity can vary among spatial scales and taxa.ObjectivesTo design biodiversity-friendly landscapes, we use nationwide bird survey data and land use maps to examine the effects of compositional heterogeneity, configurational heterogeneity, and habitat amount at different scales on the species richness of different bird groups.MethodsWe examine the effects of configurational heterogeneity (measured using edge density), compositional heterogeneity (Shannon’s diversity index of habitat types), and habitat amount (proportion of forest and farmland cover) at both transect (local) and landscape (0.5, 1, or 2 km) scales on the species richness of all breeding birds, forest birds, farmland birds, and introduced birds.ResultsTotal species richness had a hump-shaped relationship with local forest cover, and with farmland cover at landscape scale. Richness of both forest birds and richness of farmland birds increased with Shannon’s diversity index of habitat types at both local and landscape scales, but only increased with the amount of their preferred habitat at the local scale. Richness of introduced birds was greater in landscapes with higher edge density, suggesting those species are associated with human-dominated landscapes.ConclusionsHigh compositional heterogeneity with low configurational heterogeneity at the landscape scale may help maintain native bird richness while minimising the spread of introduced species in Taiwan. These results can help guide land use planning to achieving biodiversity goals in a country with intensive land-use competition.
Stepping dynamics of dynein characterized by MINFLUX
Authors: Slivka Joseph , Gleave Emma , Wijewardena Devinda P. , Canty John T. , Selvin Paul R. , Carter Andrew P. , Yildiz Ahmet 
Published: July 2024

AbstractCytoplasmic dynein is a dimeric motor that drives minus-end directed transport on microtubules (MTs). To couple ATP hydrolysis to a mechanical step, a dynein monomer must be released from the MT before undergoing a conformational change that generates a bias towards the minus end. However, the dynamics of dynein stepping have been poorly characterized by tracking flexible regions of the motor with limited resolution. Here, we developed a cysteine-light mutant of yeast dynein and site-specifically labeled its MT-binding domain in vitro. MINFLUX tracking at sub-millisecond resolution revealed that dynein hydrolyzes one ATP per step and takes multitudes of 8 nm steps at physiological ATP. Steps are preceded by the transient movement towards the plus end. We propose that these backward “dips” correspond to MT release and subsequent diffusion of the stepping monomer around its MT-bound partner before taking a minus-end-directed conformational change of its linker. Our results reveal the order of sub-millisecond events that result in a productive step of dynein.
Queens from a unique hyper-denseLasius nigerpopulation tolerate pleometrosis better than queens from a ‘normal’ population
Authors: Stukalyuk Stanislav , Czaczkes Tomer 
Published: July 2024

AbstractThe claustral, monogynous antLasius nigeroften founds colonies pleometrotically (with two or more queens), but later aggression from queens or workers can result in the death of all but one queen. Recently, a hyper-dense population ofL. nigerwas discovered, showing minimal worker-worker aggression and interconnected colonies. Here, we ask whether queens are more tolerant of conspecifics in a pleometrotic setting. We collected queens directly after a nuptial flight from both the hyper-dense population and a ‘normal’ population, maintained them in pleometrotic groups, and followed queen survival for 227 days. While queens from the ‘normal’ population showed poor survival (under 20% survival after 130 days), resulting in usually one queen per pleometrotic group, 75% of queens from the hyperdense population survived to 227 days. Mortality in the ‘normal’ population was not centered around the emergence of the first workers. While the colonies from the hyper-dense population are all monogynous, this tolerance of pleometrosis may be linked to their apparent intraspecific tolerance and may be a step towards unicoloniality.
The microRNA156/SPL9module mediates auxin response to facilitate apical hook maintenance inArabidopsis
Authors: Pierdona Flaviani G. , de Moraes Silva Ana Julia , Vicente Mateus Henrique , Taylor Laura , Pedmale Ullas , Nogueira Fabio T. S. 
Published: July 2024

ABSTRACTAuxin coordinates cell growth by promoting or inhibiting cell expansion during etiolated seedling development, but whether and how microRNA modules participate in this process remains unclear. Here, we show the miRNA156/SQUAMOSA PROMOTER-BINDING-PROTEIN-LIKE9(miR156/SPL9) module is critical for skotomorphogenesis. Perturbation of the miR156/SPL9module affected skotomorphogenesis, as the loss of miR156 function orSPL9de-repression led to shorter hypocotyl, higher hook angle, and delayed hook opening. Opposing phenotypes were observed in dark-grownspl9and miR156-overexpressing seedlings. Importantly, loss of miR156-dependentSPL9regulation triggered apical hook formation even under reduced levels of endogenous auxin. miR156-targetedSPL9arrested cell expansion by repressingsmall auxin-up RNA19(SAUR19) gene in aFRUITFULL(FUL)-dependent and independent manner. The conserved miR156/SPL9/15module also affects skotomorphogenesis in tomato, impacting its successful soil emergence. Our findings unravel how the miR156/SPL9module plays a pivotal role in the auxin network coordinating apical hook development to enable appropriate seedling emergence.
A ternary Neurexin-T178-PTPR complex represents a core-module of neuronal synapse organization
Authors: Thivaios Spyros , Schwenk Jochen , Brechet Aline , Boudkkazi Sami , Henneken Phil , Kocylowski Maciej K. , Haupt Alexander , Kaminski Debora , van den Broucke Jean-Baptiste , Schreiner Dietmar , Schulte Uwe , Sterky Fredrik H. , Yuzaki Michisuke , Scheiffele Peter , Fakler Bernd 
Published: July 2024

SummaryComplexes of synaptic adhesion molecules instruct the formation, functional specification and plasticity of neuronal synapses. Proteomic and candidate gene studies have identified an array of synaptic adhesion molecules that may cooperate or provide independent columns connecting synaptic compartments, thereby, promoting the nucleation of presynaptic active zones and recruitment of postsynaptic neurotransmitter receptors.Here, we used a systematic large-scale multi-epitope affinity-purification approach (total of >120 purifications with 30 target proteins), combined with quantitative mass spectrometry to comprehensively map trans-synaptic protein networks in the mouse brain. We discover a universal presynaptic core-module consisting of the neurexin proteins and LAR-type receptor protein tyrosine phosphatases (PTPRD,S,F), linked by the tetraspanin proteins T178A, B. These ternary Neurexin-T178-PTPR complexes form through their trans-membrane domains and assemble during biogenesis in the ER. Loss of T178B results in module dissociation and loss of LAR-PTPRs. At synapses, the Neurexin-T178-PTPR module recruits stable trans-synaptic protein networks with specific pre- and post-synaptic partners and secreted extracellular linkers. These networks encompass stable associations with unique postsynaptic GABAergic and glutamatergic neurotransmitter receptor complexes, identifying the Neurexin-T178-PTPR module as a central, universal integrator of trans-synaptic signaling in the central nervous system.
Untargeted metabolomics reveals anion and organ-specific biochemistry of salinity tolerance in willow
Authors: Sas Eszter , Frémont Adrien , Gonzalez Emmanuel , Sarrazin Mathieu , Barnabé Simon , Labrecque Michel , Brereton Nicholas James Beresford , Pitre Frédéric Emmanuel 
Published: July 2024

1AbstractWillows can alleviate soil salinisation while generating sustainable feedstock for biorefinery, yet the metabolomic adaptations underlying their salt tolerance remain poorly understood. Testing two environmentally abundant salts, the response ofSalix miyabeanawas assessed after treatment with a moderate concentration of NaCl, and both moderate and high concentrations of Na2SO4in a 12-week pot trial. Willows tolerated salts across all treatments (up to 9.1dS m-1soil ECe), maintaining photosynthesis and biomass while selectively partitioning ions, confining Na+to roots and accumulating Cl-and SO2-in the canopy, and adapting to osmotic stress via reduced stomatal conductance. Untargeted LC-MS/MS captured over 5,000 putative compounds, characterising the baseline willow metabolome, including 278 core compounds constitutively produced across organs. Comparative statistical analyses revealed widespread metabolic reprogramming in response to soil salinity, altering 28% of the overall metabolome, and highlighting organ-tailored regulation. Comparing both salt forms at equimolar sodium, generalised salinity responses were limited to 3% of the metabolome, predominantly in roots. Anion-specific metabolomic responses were more extensive, with NaCl reducing carbohydrates and TCA intermediates, thereby exerting pressure on carbon and energy resources, alongside the accumulation of root structuring compounds, antioxidants flavonoids, and fatty acids. In contrast, Na2SO4salinity triggered accumulation of sulphur-containing larger peptides, suggesting that excess sulphate incorporation leverage ion toxicity to produce specialized salt-tolerance associated metabolites. This high-depth picture of the willow metabolome underscores the importance of capturing plant adaptations to salt stress at organ-scale and considering ion-specific contributions to soil salinity.
Reprograming gene expression in “hibernating”C. elegansinvolves the IRE-1/XBP-1 pathway
Authors: Engelfriet Melanie L. , Guo Yanwu , Arnold Andreas , Valen Eivind , Ciosk Rafal 
Published: July 2024

ABSTRACTIn nature, many animals respond to cold by entering hibernation, while in clinical settings, controlled cooling is used in transplantation and emergency medicine. However, the molecular mechanisms that enable cells to survive severe cold are still not fully understood. One key aspect of cold adaptation is the global downregulation of protein synthesis. Studying it in the nematodeCaenorhabditis elegans, we find that the translation of most mRNAs continues in the cold, albeit at a slower rate, and propose that cold-specific gene expression is regulated primarily at the transcription level. Supporting this idea, we found that the transcription of certain cold-induced genes is linked to the activation of unfolded protein response (UPR) through the conserved IRE-1/XBP-1 signaling pathway. Our findings suggest that this pathway is triggered by cold-induced perturbations in proteins and lipids within the endoplasmic reticulum, and that its activation is beneficial for cold survival.
Analysis of mixtures of birds and insects in weather radar data
Authors: Shi Xu , Drucker Jacob , Chapman Jason W. , Sanchez Herrera Melissa , Dokter Adriaan M. 
Published: July 2024

AbstractWeather radars are increasingly used to study the spatial-temporal dynamics of airborne birds and insects. These two taxa often co-occur and separating their contributions remains a major analytical challenge. Most studies have restricted analyses to locations, seasons, and periods when one or the other taxa dominates. In this study, we describe an analytical method to estimate the proportion of birds and insects from vertical profiles of biological reflectivities, using a minimal number of assumptions on the airspeeds of birds and insects. We evaluated our method on understudied regions where airborne insect density is too high for existing approaches of studying bird migration with weather radars: the tropics (Colombia) and the southern temperate zone (Southeast Australia). Our method estimates that bird and insect signals routinely reach similar magnitudes in these regions. Retrieved patterns across daily and annual cycles reflected expected biological patterns that are indicative of migratory and non-migratory movements in both climates and migration systems. Compared to fixed airspeed thresholding, we obtain finer separation and retain more spatial-temporal complexity that is crucial to revealing aerial habitat use of both taxa. Our analytical procedure is readily implemented into existing software, empowering ecologists to explore aerial ecosystems outside the northern temperate zone, as well as diurnal migration of birds and insects that remains heavily understudied.Lay summaryWe developed a new method to differentiate between birds and insects in weather radar data.This method uses minimal assumptions about the flight speeds of birds and insects.We tested the method in regions with high insect density: the tropics (Colombia) and southern temperate zone (Southeast Australia).Our method estimated proportions of birds and insects that captured expected patterns of daily and annual movements, which were indicative of migratory and non-migratory movement of both taxa.Unlike fixed airspeed criteria for bird and insect separation, our approach provides a more detailed understanding of aerial habitat use by both birds and insects.This method can be easily added to existing software, helping ecologists study bird and insect movements in less-studied areas and ecosystems.