bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation and outcome of minimally invasive pancreatoduodenectomy in Europe: a registry-based retrospective study – a critical appraisal of the first 3 years of the E-MIPS registry
Authors: Emmen Anouk M.L.H. , de Graaf Nine , Khatkov I.E. , Busch O.R. , Dokmak S. , Boggi Ugo , Groot Koerkamp Bas , Ferrari Giovanni , Molenaar I.Q. , Saint-Marc Olivier , Ramera Marco , Lips Daan J. , Mieog J.S.D. , Luyer Misha D.P. , Keck Tobias , D’Hondt Mathieu , Souche F.R. , Edwin Bjørn , Hackert Thilo , Liem M.S.L. , Iben-Khayat Abdallah , van Santvoort H.C. , Mazzola Michele , de Wilde Roeland F. , Kauffmann E.F. , Aussilhou Beatrice , Festen Sebastiaan , Izrailov R. , Tyutyunnik P. , Besselink M.G. , Abu Hilal Mohammad ,   for the European Consortium on Minimally Invasive Pancreatic Surgery (E-MIPS)
Published: January 2024

Background:
International multicenter audit-based studies focusing on the outcome of minimally invasive pancreatoduodenectomy (MIPD) are lacking. The European Registry for Minimally Invasive Pancreatic Surgery (E-MIPS) is the E-AHPBA endorsed registry aimed to monitor and safeguard the introduction of MIPD in Europe.

Materials and Methods:
A planned analysis of outcomes among consecutive patients after MIPD from 45 centers in 14 European countries in the E-MIPS registry (2019–2021). The main outcomes of interest were major morbidity (Clavien–Dindo grade ≥3) and 30-day/in-hospital mortality.

Results:
Overall, 1336 patients after MIPD were included [835 robot-assisted (R-MIPD) and 501 laparoscopic MIPD (L-MIPD)]. Overall, 20 centers performed R-MIPD, 15 centers L-MIPD, and 10 centers both. Between 2019 and 2021, the rate of centers performing L-MIPD decreased from 46.9 to 25%, whereas for R-MIPD this increased from 46.9 to 65.6%. Overall, the rate of major morbidity was 41.2%, 30-day/in-hospital mortality 4.5%, conversion rate 9.7%, postoperative pancreatic fistula grade B/C 22.7%, and postpancreatectomy hemorrhage grade B/C 10.8%. Median length of hospital stay was 12 days (IQR 8–21). A lower rate of major morbidity, postoperative pancreatic fistula grade B/C, postpancreatectomy hemorrhage grade B/C, delayed gastric emptying grade B/C, percutaneous drainage, and readmission was found after L-MIPD. The number of centers meeting the Miami Guidelines volume cut-off of ≥20 MIPDs annually increased from 9 (28.1%) in 2019 to 12 (37.5%) in 2021 (P=0.424). Rates of conversion (7.4 vs. 14.8% P<0.001) and reoperation (8.9 vs. 15.1% P<0.001) were lower in centers, which fulfilled the Miami volume cut-off.

Conclusion:
During the first 3 years of the pan-European E-MIPS registry, morbidity and mortality rates after MIPD were acceptable. A shift is ongoing from L-MIPD to R-MIPD. Variations in outcomes between the two minimally invasive approaches and the impact of the volume cut-off should be further evaluated over a longer time period.
Racial inequities in HIV incidence among men who have sex with men prior to and amidst an Ending the HIV Epidemic initiative
Authors: Jamison Kelly E. , Braunstein Sarah L. , Pathela Preeti 
Published: January 2024

Objective:
The aim of this study was to examine trends in HIV incidence among men who have sex with men (MSM) relative to the scale up of Ending the HIV Epidemic (EHE) initiatives, including biomedical prevention strategies, and to describe racial inequities over time.

Design:
A cross-sectional study, matching annual cohorts of New York City (NYC) Sexual Health Clinic (SHC) patients from 2010 to 2018 to the citywide HIV registry to identify seroconversions during 1 year of follow-up, through 2019.

Methods:
We examined HIV incidence for each annual cohort of MSM using diagnoses within 1 year after last negative HIV test. We calculated incidence rates and rate ratios (IRR) pooled across 3-year intervals (2010–2012, 2013–2015, 2016–2018) by race/ethnicity, age, neighborhood poverty level, recent STI diagnosis, and condom use during anal sex.

Results:
There were 36 156 study visits among MSM attending NYC SHCs, including 37% among White MSM and 63% among MSM of color. From 2010 to 2018, HIV incidence decreased overall from 2.82 to 0.82/100 person-years, and among all race/ethnicity, age, poverty, STI, and condom use subgroups. For 2010–2012 vs. 2016–2018, adjusted IRRs (95% CI) increased for Black MSM [1.8 (1.3–2.6) vs. 6.0 (3.5–10.2)], Latino MSM [1.4 (1.0–2.0) vs. 4.0 (2.3–6.8)], and MSM of other races [1.0 (0.6–1.7) vs. 2.5 (1.3–4.9)] compared with White MSM. Black and Latino MSM seroconverted at significantly higher rates than White MSM in the same age groups and neighborhood poverty level.

Conclusion:
Despite decreases in HIV incidence among MSM, racial inequities were exacerbated over time. Addressing structural factors that impact racial inequities in risk of HIV should undergird EHE initiatives.
Association Between Anesthesiologist Sex and Patients’ Postoperative Outcomes: A Population-based Cohort Study
Authors: Jerath Angela , Satkunasivam Raj , Kaneshwaran Kirusanthy , Aminoltejari Khatereh , Chang Ashton , MacDonell D. Su-Yin , Kealey Alayne , Ladowski Stephanie , Sarmah Anita , Flexman Alana M. , Lorello Gianni R. , Nabecker Sabine , Coburn Natalie , Conn Lesley Gotlib , Klaassen Zachary , Ranganathan Sanjana , Riveros Carlos , McCartney Colin J.L. , Detsky Allan S. , Wallis Christopher J.D. 
Published: January 2024

Objective:
To examine the association of anesthesiologist sex on postoperative outcomes.

Summary Background Data:
Differences in patient postoperative outcomes exist, depending on whether the primary surgeon is male or female, with better outcomes seen among patients treated by female surgeons. Whether the intraoperative anesthesiologist’s sex is associated with differential postoperative patient outcomes is unknown.

Methods:
We performed a population-based, retrospective cohort study among adult patients undergoing one of 25 common elective or emergent surgical procedures from 2007–2019 in Ontario, Canada. We assessed the association between sex of the intraoperative anesthesiologist and the primary endpoint of adverse postoperative outcome, defined as death, readmission, or complication within 30-days following surgery using generalized estimating equations.

Results:
Among 1,165,711 patients treated by 3,006 surgeons and 1,477 anesthesiologists, 311,822 (26.7%) received care from a female anesthesiologist and 853,889 (73.3%) from a male anesthesiologist. Overall, 10.8% of patients experienced one or more adverse postoperative outcomes of whom 1.1% died. Multivariable adjusted rates of the composite primary endpoint were higher among patients treated by male anesthesiologists (10.6%) compared to female anesthesiologists (10.4%; adjusted odds ratio 1.02, 95% CI 1.00-1.05, P=0.048).

Conclusions:
We demonstrated a significant association between sex of the intraoperative anesthesiologist and patient short-term outcomes after surgery in a large cohort study. This study supports growing literature of improved patient outcomes among female practitioners. The underlying mechanisms of why outcomes differ between male and female physicians remain elusive and require further in-depth study.
Nano Colonies: Rearing honey bee queens and their offspring in small laboratory arenas
Authors: Lamas Zachary S. , Solmaz Serhat , Stevens Cory , Bragg Jason , Ryabov Eugene V. , Madella Shayne , Corona Miguel , Evans Jay D. 
Published: January 2024

AbstractHoney bees create complex societies of self-organized individuals in intricate colonies. Studies of honey bees are carried out in both the field and the laboratory. However, field research is encumbered by the difficulties of making reliable observations and environmental confounders. Meanwhile, laboratory trials produce data that are not field realistic as they lack key characteristics of a natural colony. Additionally, advances in honey bee research have been hindered without reliable methodology to rear queens in the laboratory. Here we provide a new system to reliably produce queens and worker brood in the laboratory and describe how this system fits with artificial insemination of queens as a step towards a continuous self-contained source of bees. The process creates a bridge between field research and laboratory trials and provides a secure system for contagious or regulated elements while maintaining many of the intrinsic characteristics of a honey bee colony.
DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model
Authors: Wang Xiao , Zhu Han , Terashi Genki , Taluja Manav , Kihara Daisuke 
Published: January 2024

AbstractCryogenic electron microscopy (cryo-EM) has now been widely used for determining multi-chain protein complexes. However, modeling a complex structure is challenging particularly when the map resolution is low, typically in the intermediate resolution range of 5 to 10 Å. Within this resolution range, even accurate structure fitting is difficult, let alone de novo modeling. To address this challenge, here we present DiffModeler, a fully automated method for modeling protein complex structures. DiffModeler employs a diffusion model for backbone tracing and integrates AlphaFold2-predicted single-chain structures for structure fitting. Extensive testing on cryo-EM maps at intermediate resolutions demonstrates the exceptional accuracy of DiffModeler in structure modeling, achieving an average TM-Score of 0.92, surpassing existing methodologies significantly. Notably, DiffModeler successfully modeled a protein complex composed of 47 chains and 13,462 residues, achieving a high TM-Score of 0.94. Further benchmarking at low resolutions (10-20 Å) confirms its versatility, demonstrating plausible performance. Moreover, when coupled with CryoREAD, DiffModeler excels in constructing protein-DNA/RNA complex structures for near-atomic resolution maps (0-5 Å), showcasing state-of-the-art performance with average TM-Scores of 0.88 and 0.91 across two datasets.
An active light signalling pathway is necessary for ABA-induced inhibition of hypocotyl elongation
Authors: Cañibano Esther , Soto-Gomez Daniela , Oliveros Juan Carlos , Bourbousse Clara , Fonseca Sandra 
Published: January 2024

AbstractDriven by cell elongation, hypocotyl growth is tightly controlled by light and responds to external stimuli and endogenous hormonal pathways. Hypocotyls are known to be responsive to the stress signalling hormone abscisic acid (ABA) which effectively inhibits cell elongation, but how this regulation is connected to light responses and other endogenous hormonal pathways has been a subject of limited studies. Here, we show that whereas hypocotyl elongation is sensitive to ABA in light-grown seedlings, the hypocotyl of dark-grown etiolated seedlings is ABA-insensitive. In the dark, hypocotyl sensitivity to ABA is restored in the constitutive photomorphogenicpifqandcop1-4mutants, suggesting that an active light signalling pathway is necessary for hypocotyl responsiveness to ABA. However, etiolated hypocotyls retain ABA responsiveness, as could be detected by the induction ofABI1andRD29Btranscripts in response to exogenous ABA, suggesting that inhibition of hypocotyl elongation mediated by ABA does not follows the canonical ABA signalling dependent on transcription. Here, using RNA-seq analysis we identified a number of ABA differentially expressed genes (DEGs) that correlate with ABA inhibition of hypocotyl elongation, specifically in dark-grownpifqor light-grown WT plants, and whose expression remains unchanged by ABA treatment in dark-grown WT plants. Among these DEGs we identified a number of genes playing a role in cell elongation directly at the level of the plasma membrane, as SAURs, ion transporters, auxin flux regulators, channels, and cell wall modification enzymes. The use of the auxin transport inhibitor, NPA, revealed that in the light auxin transport impairment renders hypocotyls insensitive to ABA in WT andpifqplants. Thus, in the light, hypocotyl responsiveness to ABA is dependent on auxin transport and independent of PIFs. In the dark, PIFs render hypocotyls insensitive to ABA, perhaps by regulating the expression of a number of ABA DEGs, a mechanism that could allow plants to prioritize the elongation towards light, avoiding to slow-down soil emergence that could be induced by ABA signalling in case of sudden reduction of soil moisture.
Can overlooking ‘invisible landscapes’ bias habitat selection estimation and population distribution projections?
Authors: Dejeante Romain , Lemaire-Patin Rémi , Chamaillé-Jammes Simon 
Published: January 2024

ABSTRACTSpecies’ future distributions are commonly predicted using models that link the likelihood of occurrence of individuals to the environment. Although animals’ movements are influenced by physical landscapes and individual experiences (for example space familiarity), species distribution models developed from observations of unknown individuals cannot integrate these latter variables, turning them into ‘invisible landscapes’. In this theoretical study, we address how overlooking ‘invisible landscapes’ impacts the estimation of habitat selection and thereby the projection of future distributions. Overlooking the attraction towards some ‘invisible’ variable consistently led to over-estimating the strength of habitat selection. Consequently, projections of future population distributions were also biased, with animals tracking habitat changes less than predicted. Our results reveal an overlooked challenge faced by correlative species distribution models based on the observation of unknown individuals, whose past experience of the environment is by definition not known. Mechanistic distribution modelling integrating cognitive processes underlying movement should be developed.
Provisioning polyethylene glycol (PEG) to large herbivores in nutrient poor savannas can break food limitation
Authors: Schroder Bradley , Van Langevelde Frank , Schroder Nicola-Anne Hawkins , Prins Herbert H. T. 
Published: January 2024

AbstractReproduction and survival of herbivores in nutrient poor savannas is low due to low nutrient and energy availability, partly caused by high levels of tannins. Polyethylene glycol (PEG) increases the availability of proteins for herbivores by binding tannins. The effect of PEG on the diet of free-roaming herbivores has not been tested. Our hypothesis was deploying lick blocks with the addition of PEG in a nutrient poor savanna, will result in a broadening of the diet of free-roaming herbivores with higher percentages of browse species and higher utilisation per browse species, with higher tannin levels. We further hypothesised that the mineral content in the faeces, once exposed to PEG would increase. We collected faecal samples of five herbivore species with various feeding methods (grazers, browsers or mixed feeders). The study used a Before-After-Control-Impact (BACI) design. The results show that the addition of PEG promotes a change in the browse dietary choices of four of the five herbivore species, and are expressed as a broader choice of diet, coupled with higher numbers of browse species with low edibility and higher tannin levels. The addition of PEG had no noteworthy effect on the concentration of minerals found in the faeces.
Studying self-assembly of norovirus capsid by a combination ofin silicomethods
Authors: Carvaillo Jean-Charles , Tubiana Thibault , Detchanamourtty Sella , Bressanelli Stéphane , Barroso da Silva Fernando Luís , Boulard Yves 
Published: January 2024

AbstractUnderstanding how macromolecular assembly occurs is a fundamental and challenging problem because spontaneous, precise assembly is at the center of most biological processes. It is an elaborate process that requires non-covalent stable interactions between partners to stabilize the desired architecture for a specific purpose. One of the advantages of virus models is that under adequate conditions capsid proteins can be efficiently assembledin vitroin the absence of any other component, providing simplified experimental models that can be rigorously characterized. The present study aims at describing the initial steps of molecular self-assembly of norovirus-like particles (NoVLPs, composed solely of the major norovirus capsid protein VP1), by combiningin silicocomputational approaches to explore complementary physical properties. We show that this strategy allows not only recapitulating but also revising a former NoVLP assembly model. Our approach can be applied and extended to other problems in macromolecular assembly.
Unravelling Different Biological Roles Of Plant Synaptotagmins
Authors: García-Hernández Selene , Rubio Lourdes , Pérez-Sancho Jessica , Esteban del Valle Alicia , Benítez-Fuente Francisco , Beuzón Carmen R. , Macho Alberto P. , Ruiz-López Noemi , Albert Armando , Botella Miguel A. 
Published: January 2024

ABSTRACTEndoplasmic Reticulum-Plasma Membrane contact sites (ER-PM CS) are evolutionarily conserved membrane domains found in all eukaryotes, where the endoplasmic reticulum (ER) closely interfaces with the plasma membrane (PM). This short distance, typically 10-30 nm, is achieved in Arabidopsis through the action of tether proteins such as Synaptotagmins (SYTs). Arabidopsis comprises five SYT members (SYT1-SYT5), but whether they possess overlapping or distinct biological functions remains elusive.SYT1is the best-characterized gene member and plays an essential role in the resistance to abiotic stress. This study reveals that while the functionally redundantSYT1andSYT3genes are involved in salt and cold stress resistance,SYT5is associated withPseudomonas syringaeresistance despite evidence ofin vivointeraction between SYT1 and SYT5. Structural phylogenetic analysis indicates that SYT1 and SYT5 clades emerged early in the evolution of land plants. These protein clades exhibit different structural features, rationalizing their distinct biological roles.
The Investigation of Somatostatin Receptors as a Potential Target in Breast Phyllodes Tumours
Authors: Süer Mickler Hande , Erkan Murat Mert 
Published: January 2024

ABSTRACTSomatostatin receptors (SSTRs) constitute a family of G protein-coupled receptors that modulate hormonal secretion and regulate cell proliferation and apoptosis upon binding with somatostatin or its synthetic analogues. SSTRs are expressed in most neuroendocrine neoplasms, particularly in gastroenteropancreatic neuroendocrine tumours, and have been utilized as diagnostic markers as well as therapeutic targets. The radioiodinated somatostatin analogue 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid-Tyr3-octreotate (DOTATATE) has been employed for SSTR-targeting for either diagnostic or therapeutic purposes depending on the labelling with68Gallium or177Lutetium, respectively.SSTR expression is reported in a subset of breast adenocarcinoma and breast neuroendocrine carcinomas; however, minimal knowledge exists regarding their expression in fibroepithelial (biphasic) breast lesions such as fibroadenoma and phyllodes tumours. Aggressive ends of the spectrum, i.e. “cystosarcoma phyllodes” may present a management challenge with recurrences and metastases. In this exploratory study, we investigated both gene and protein expression of SSTR in fibroepithelial lesions of the breast. Our findings reveal that both fibroadenoma and phyllodes tumours express SSTRs. Immunohistochemical analyses suggested that this expression is in the stromal, not epithelial, component by demonstrating that SSTR is predominantly expressed in the areas overlapping with α-smooth muscle actin-positive myoepithelial cells around blood vessels and capillary structures. This study is the first in the literature to demonstrate SSTR positivity in mammary fibroepithelial neoplasms., In a patient undergoing a gallium scan, which is widely used in clinical practice, if a positive lesion is discovered in the breast, the possibility of a fibroadenoma or phyllodes tumour needs to be considered. Once validated, these findings may also have significant implications for the management of these tumours.
Characterization of Cancer Stem Cells in Laryngeal Squamous Cell Carcinoma by Single-Cell RNA Sequencing
Authors: Li Yanguo , Lin Chen , Chu Yidian , Wei Zhengyu , Ding Qi , Gu Shanshan , Deng Hongxia , Liao Qi , Shen Zhisen 
Published: January 2024

AbstractCancer stem cells (CSCs) constitute a pivotal element within the tumor microenvironment (TME), driving the initiation and progression of cancer. However, the identification of CSCs and their underlying molecular mechanisms in laryngeal squamous cell carcinoma (LSCC) remains a formidable challenge. We employed single-cell RNA sequencing of matched primary tumor tissues, paracancerous tissues, and local lymph nodes from three LSCC patients. Two distinct clusters of stem cells originating from epithelial populations were delineated and verified as CSCs and normal stem cells (NSCs) respectively. CSCs were abundant in the paracancerous tissues compared to the tumor tissues. CSCs showed high expression of stem cell marker genes such asPROM1,ALDH1A1, andSOX4, and increased activity of tumor-related hypoxia, Wnt/β-catenin, and notch signaling pathways. We then explored the intricate crosstalk between CSCs and the TME cells and identified targets within the TME that related with CSCs. We also find eight marker genes of CSCs that correlated significantly with the prognosis of LSCC patients. Furthermore, bioinformatics analyses showed that drugs such as erlotinib, OSI-027, and ibrutinib selectively targeted the CSC-specifically expressed genes. In conclusion, our results represent the first comprehensive characterization of CSCs properties in LSCC at the single-cell level.
iVirP: An integrative, efficient, and user-friendly pipeline to annotate viral contigs from raw reads of metagenome or VLP sequencing
Authors: Li Bowen , Jiao Xianyue , Liang Guanxiang 
Published: January 2024

AbstractMetagenome sequencing and virus-like particles sequencing make it possible to explore the virome in the humans and other organisms. One way to analyze the sequencing data is to assemble reads into contigs according to the overlapping regions, and then the predicted viral contigs are screened out to conduct deeper dives. iVirP (integrative virome pipeline) is a user-friendly pipeline that includes the whole process of viral contigs discovery from the quality control of raw data to the filter of high quality viral contigs. This pipeline also features a branching function that can estimate the abundance of known eukaryotic viruses in a short period, while reducing host contamination. It is suitable for the rapid diagnosis of pathogens. Throughout iVirP, many details that might affect the experience of users are optimized carefully to reduce the time spent on dealing with usage and errors. iVirP was tested on a published, high-quality VLP sequencing dataset and was able to well reproduce the conclusions of the corresponding research. The benchmark indicates that iVirP could accurately assemble viral contigs from real sequencing data. iVirP is easy to install and currently available athttps://github.com/li-bw18/iVirP.