bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Medical Segmentation Decathlon
Authors: Antonelli Michela , Reinke Annika , Bakas Spyridon , Farahani Keyvan , Kopp-Schneider Annette , Landman Bennett A. , Litjens Geert , Menze Bjoern , Ronneberger Olaf , Summers Ronald M. , van Ginneken Bram , Bilello Michel , Bilic Patrick , Christ Patrick F. , Do Richard K. G. , Gollub Marc J. , Heckers Stephan H. , Huisman Henkjan , Jarnagin William R. , McHugo Maureen K. , Napel Sandy , Pernicka Jennifer S. Golia , Rhode Kawal , Tobon-Gomez Catalina , Vorontsov Eugene , Meakin James A. , Ourselin Sebastien , Wiesenfarth Manuel , Arbeláez Pablo , Bae Byeonguk , Chen Sihong , Daza Laura , Feng Jianjiang , He Baochun , Isensee Fabian , Ji Yuanfeng , Jia Fucang , Kim Ildoo , Maier-Hein Klaus , Merhof Dorit , Pai Akshay , Park Beomhee , Perslev Mathias , Rezaiifar Ramin , Rippel Oliver , Sarasua Ignacio , Shen Wei , Son Jaemin , Wachinger Christian , Wang Liansheng , Wang Yan , Xia Yingda , Xu Daguang , Xu Zhanwei , Zheng Yefeng , Simpson Amber L. , Maier-Hein Lena , Cardoso M. Jorge 
Published: July 2022

AbstractInternational challenges have become the de facto standard for comparative assessment of image analysis algorithms. Although segmentation is the most widely investigated medical image processing task, the various challenges have been organized to focus only on specific clinical tasks. We organized the Medical Segmentation Decathlon (MSD)—a biomedical image analysis challenge, in which algorithms compete in a multitude of both tasks and modalities to investigate the hypothesis that a method capable of performing well on multiple tasks will generalize well to a previously unseen task and potentially outperform a custom-designed solution. MSD results confirmed this hypothesis, moreover, MSD winner continued generalizing well to a wide range of other clinical problems for the next two years. Three main conclusions can be drawn from this study: (1) state-of-the-art image segmentation algorithms generalize well when retrained on unseen tasks; (2) consistent algorithmic performance across multiple tasks is a strong surrogate of algorithmic generalizability; (3) the training of accurate AI segmentation models is now commoditized to scientists that are not versed in AI model training.
Trigger factor both holds and folds its client proteins
Authors: Wu Kevin , Minshull Thomas C. , Radford Sheena E. , Calabrese Antonio N. , Bardwell James C. A. 
Published: July 2022

AbstractATP-independent chaperones like trigger factor are generally assumed to play passive roles in protein folding by acting as holding chaperones. Here we show that trigger factor plays a more active role. Consistent with a role as an aggregation inhibiting chaperone, we find that trigger factor rapidly binds to partially folded glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and prevents it from non-productive self-association by shielding oligomeric interfaces. In the traditional view of holding chaperone action, trigger factor would then be expected to transfer its client to a chaperone foldase system for complete folding. Unexpectedly, we noticed that GAPDH folds into a monomeric but otherwise rather native-like intermediate state while trigger factor-bound. Upon release from trigger factor, the mostly folded monomeric GAPDH rapidly self-associates into its native tetramer and acquires enzymatic activity without needing additional folding factors. The mechanism we propose here for trigger factor bridges the holding and folding activities of chaperone function.
Constrained CMIP6 projections indicate less warming and a slower increase in water availability across Asia
Authors: Chai Yuanfang , Yue Yao , Slater Louise J. , Yin Jiabo , Borthwick Alistair G. L. , Chen Tiexi , Wang Guojie 
Published: July 2022

AbstractClimate projections are essential for decision-making but contain non-negligible uncertainty. To reduce projection uncertainty over Asia, where half the world’s population resides, we develop emergent constraint relationships between simulated temperature (1970–2014) and precipitation (2015–2100) growth rates using 27 CMIP6 models under four Shared Socioeconomic Pathways. Here we show that, with uncertainty successfully narrowed by 12.1–31.0%, constrained future precipitation growth rates are 0.39 ± 0.18 mm year−1 (29.36 mm °C−1, SSP126), 0.70 ± 0.22 mm year−1 (20.03 mm °C−1, SSP245), 1.10 ± 0.33 mm year−1 (17.96 mm °C−1, SSP370) and 1.42 ± 0.35 mm year−1 (17.28 mm °C−1, SSP585), indicating overestimates of 6.0–14.0% by the raw CMIP6 models. Accordingly, future temperature and total evaporation growth rates are also overestimated by 3.4–11.6% and −2.1–13.0%, respectively. The slower warming implies a lower snow cover loss rate by 10.5–40.2%. Overall, we find the projected increase in future water availability is overestimated by CMIP6 over Asia.
Hepatic non-parenchymal S100A9-TLR4-mTORC1 axis normalizes diabetic ketogenesis
Authors: Ursino Gloria , Ramadori Giorgio , Höfler Anna , Odouard Soline , Teixeira Pryscila D. S. , Visentin Florian , Veyrat-Durebex Christelle , Lucibello Giulia , Firnkes Raquel , Ricci Serena , Vianna Claudia R. , Jia Lin , Dirlewanger Mirjam , Klee Philippe , Elmquist Joel K. , Roth Johannes , Vogl Thomas , Schwitzgebel Valérie M. , Jornayvaz François R. , Boland Andreas , Coppari Roberto 
Published: July 2022

AbstractUnrestrained ketogenesis leads to life-threatening ketoacidosis whose incidence is high in patients with diabetes. While insulin therapy reduces ketogenesis this approach is sub-optimal. Here, we report an insulin-independent pathway able to normalize diabetic ketogenesis. By generating insulin deficient male mice lacking or re-expressing Toll-Like Receptor 4 (TLR4) only in liver or hepatocytes, we demonstrate that hepatic TLR4 in non-parenchymal cells mediates the ketogenesis-suppressing action of S100A9. Mechanistically, S100A9 acts extracellularly to activate the mechanistic target of rapamycin complex 1 (mTORC1) in a TLR4-dependent manner. Accordingly, hepatic-restricted but not hepatocyte-restricted loss of Tuberous Sclerosis Complex 1 (TSC1, an mTORC1 inhibitor) corrects insulin-deficiency-induced hyperketonemia. Therapeutically, recombinant S100A9 administration restrains ketogenesis and improves hyperglycemia without causing hypoglycemia in diabetic mice. Also, circulating S100A9 in patients with ketoacidosis is only marginally increased hence unveiling a window of opportunity to pharmacologically augment S100A9 for preventing unrestrained ketogenesis. In summary, our findings reveal the hepatic S100A9-TLR4-mTORC1 axis in non-parenchymal cells as a promising therapeutic target for restraining diabetic ketogenesis.
The surfaceome of multiple myeloma cells suggests potential immunotherapeutic strategies and protein markers of drug resistance
Authors: Ferguson Ian D. , Patiño-Escobar Bonell , Tuomivaara Sami T. , Lin Yu-Hsiu T. , Nix Matthew A. , Leung Kevin K. , Kasap Corynn , Ramos Emilio , Nieves Vasquez Wilson , Talbot Alexis , Hale Martina , Naik Akul , Kishishita Audrey , Choudhry Priya , Lopez-Girona Antonia , Miao Weili , Wong Sandy W. , Wolf Jeffrey L. , Martin Thomas G. , Shah Nina , Vandenberg Scott , Prakash Sonam , Besse Lenka , Driessen Christoph , Posey Avery D. , Mullins R. Dyche , Eyquem Justin , Wells James A. , Wiita Arun P. 
Published: July 2022

AbstractThe myeloma surface proteome (surfaceome) determines tumor interaction with the microenvironment and serves as an emerging arena for therapeutic development. Here, we use glycoprotein capture proteomics to define the myeloma surfaceome at baseline, in drug resistance, and in response to acute drug treatment. We provide a scoring system for surface antigens and identify CCR10 as a promising target in this disease expressed widely on malignant plasma cells. We engineer proof-of-principle chimeric antigen receptor (CAR) T-cells targeting CCR10 using its natural ligand CCL27. In myeloma models we identify proteins that could serve as markers of resistance to bortezomib and lenalidomide, including CD53, CD10, EVI2B, and CD33. We find that acute lenalidomide treatment increases activity of MUC1-targeting CAR-T cells through antigen upregulation. Finally, we develop a miniaturized surface proteomic protocol for profiling primary plasma cell samples with low inputs. These approaches and datasets may contribute to the biological, therapeutic, and diagnostic understanding of myeloma.
Inhibition of NMDA receptors through a membrane-to-channel path
Authors: Wilcox Madeleine R. , Nigam Aparna , Glasgow Nathan G. , Narangoda Chamali , Phillips Matthew B. , Patel Dhilon S. , Mesbahi-Vasey Samaneh , Turcu Andreea L. , Vázquez Santiago , Kurnikova Maria G. , Johnson Jon W. 
Published: July 2022

AbstractN-methyl-d-aspartate receptors (NMDARs) are transmembrane proteins that are activated by the neurotransmitter glutamate and are found at most excitatory vertebrate synapses. NMDAR channel blockers, an antagonist class of broad pharmacological and clinical significance, inhibit by occluding the NMDAR ion channel. A vast literature demonstrates that NMDAR channel blockers, including MK-801, phencyclidine, ketamine, and the Alzheimer’s disease drug memantine, can bind and unbind only when the NMDAR channel is open. Here we use electrophysiological recordings from transfected tsA201 cells and cultured neurons, NMDAR structural modeling, and custom-synthesized compounds to show that NMDAR channel blockers can enter the channel through two routes: the well-known hydrophilic path from extracellular solution to channel through the open channel gate, and also a hydrophobic path from plasma membrane to channel through a gated fenestration (“membrane-to-channel inhibition” (MCI)). Our demonstration that ligand-gated channels are subject to MCI, as are voltage-gated channels, highlights the broad expression of this inhibitory mechanism.
Post-recovery COVID-19 and incident heart failure in the National COVID Cohort Collaborative (N3C) study
Authors: Salah Husam M. , Fudim Marat , O’Neil Shawn T. , Manna Amin , Chute Christopher G. , Caughey Melissa C. 
Published: July 2022

AbstractCardiac involvement has been noted in COVID-19 infection. However, the relationship between post-recovery COVID-19 and development of de novo heart failure has not been investigated in a large, nationally representative population. We examined post-recovery outcomes of 587,330 patients hospitalized in the United States (257,075 with COVID-19 and 330,255 without), using data from the National COVID Cohort Collaborative study. Patients hospitalized with COVID-19 were older (51 vs. 46 years), more often male (49% vs. 42%), and less often White (61% vs. 69%). Over a median follow up of 367 days, 10,979 incident heart failure events occurred. After adjustments, COVID-19 hospitalization was associated with a 45% higher hazard of incident heart failure (hazard ratio = 1.45; 95% confidence interval: 1.39–1.51), with more pronounced associations among patients who were younger (P-interaction = 0.003), White (P-interaction = 0.005), or who had established cardiovascular disease (P-interaction = 0.005). In conclusion, COVID-19 hospitalization is associated with increased risk of incident heart failure.
Fermi surface tomography
Authors: Borisenko Sergey , Fedorov Alexander , Kuibarov Andrii , Bianchi Marco , Bezguba Volodymyr , Majchrzak Paulina , Hofmann Philip , Baumgärtel Peter , Voroshnin Vladimir , Kushnirenko Yevhen , Sánchez-Barriga Jaime , Varykhalov Andrei , Ovsyannikov Ruslan , Morozov Igor , Aswartham Saicharan , Feia Oleh , Harnagea Luminita , Wurmehl Sabine , Kordyuk Alexander , Yaresko Alexander , Berger Helmuth , Büchner Bernd 
Published: July 2022

AbstractFermi surfaces are essential for predicting, characterizing and controlling the properties of crystalline metals and semiconductors. Angle-resolved photoemission spectroscopy (ARPES) is the only technique directly probing the Fermi surface by measuring the Fermi momenta (kF) from energy- and angular distribution of photoelectrons dislodged by monochromatic light. Existing apparatus is able to determine a number of kF -vectors simultaneously, but direct high-resolution 3D Fermi surface mapping remains problematic. As a result, no such datasets exist, strongly limiting our knowledge about the Fermi surfaces. Here we show that using a simpler instrumentation it is possible to perform 3D-mapping within a very short time interval and with very high resolution. We present the first detailed experimental 3D Fermi surface as well as other experimental results featuring advantages of our technique. In combination with various light sources our methodology and instrumentation offer new opportunities for high-resolution ARPES in the physical and life sciences.
Humanized mice for investigating sustained Plasmodium vivax blood-stage infections and transmission
Authors: Luiza-Batista Camilla , Thiberge Sabine , Serra-Hassoun Malika , Nardella Flore , Claës Aurélie , Nicolete Vanessa C. , Commère Pierre-Henri , Mancio-Silva Liliana , Ferreira Marcelo U. , Scherf Artur , Garcia Sylvie 
Published: July 2022

AbstractPlasmodium vivax is the most widespread human malaria parasite. Due to the presence of extravascular reservoirs and relapsing infections from dormant liver stages, P. vivax is particularly difficult to control and eliminate. Experimental research is hampered by the inability to maintain P. vivax cultures in vitro, due to its tropism for immature red blood cells (RBCs). Here, we describe a new humanized mice model that can support efficient human erythropoiesis and maintain long-lasting multiplication of inoculated cryopreserved P. vivax parasites and their sexual differentiation, including in bone marrow. Mature gametocytes were transmitted to Anopheles mosquitoes, which led to the formation of salivary gland sporozoites. Importantly, blood-stage P. vivax parasites were maintained after the secondary transfer of fresh or frozen infected bone marrow cells to naïve chimeras. This model provides a unique tool for investigating, in vivo, the biology of intraerythrocytic P. vivax.
Responding to eruptive transitions during the 2020–2021 eruption of La Soufrière volcano, St. Vincent
Authors: Joseph E. P. , Camejo-Harry M. , Christopher T. , Contreras-Arratia R. , Edwards S. , Graham O. , Johnson M. , Juman A. , Latchman J. L. , Lynch L. , Miller V. L. , Papadopoulos I. , Pascal K. , Robertson R. , Ryan G. A. , Stinton A. , Grandin R. , Hamling I. , Jo M-J. , Barclay J. , Cole P. , Davies B. V. , Sparks R. S. J. 
Published: July 2022

AbstractA critical challenge during volcanic emergencies is responding to rapid changes in eruptive behaviour. Actionable advice, essential in times of rising uncertainty, demands the rapid synthesis and communication of multiple datasets with prognoses. The 2020–2021 eruption of La Soufrière volcano exemplifies these challenges: a series of explosions from 9–22 April 2021 was preceded by three months of effusive activity, which commenced with a remarkably low level of detected unrest. Here we show how the development of an evolving conceptual model, and the expression of uncertainties via both elicitation and scenarios associated with this model, were key to anticipating this transition. This not only required input from multiple monitoring datasets but contextualisation via state-of-the-art hazard assessments, and evidence-based knowledge of critical decision-making timescales and community needs. In addition, we share strategies employed as a consequence of constraints on recognising and responding to eruptive transitions in a resource-constrained setting, which may guide similarly challenged volcano observatories worldwide.
A chromosome-level genome assembly of the jade perch (Scortum barcoo)
Authors: Lu Yishan , Li Ruihan , Xia Liqun , Cheng Jun , Xia Hongli , Zhan Qiuyao , Yu Dapeng , You Xinxin , Gu Ruobo , Xu Junmin , Shi Qiong , Bian Chao 
Published: July 2022

AbstractEndemic to Australia, jade perch (Scortum barcoo) is a highly profitable freshwater bass species. It has extraordinarily high levels of omega-3 polyunsaturated fatty acids (PUFAs), which detailed genes involved in are largely unclear. Meanwhile, there were four chromosome-level bass species have been previous sequenced, while the bass ancestor genome karyotypes have not been estimated. Therefore, we sequenced, assembled and annotated a genome of jade perch to characterize the detailed genes for biosynthesis of omega-3 PUFAs and to deduce the bass ancestor genome karyotypes. We constructed a chromosome-level genome assembly with 24 pairs of chromosomes, 657.7 Mb in total length, and the contig and the scaffold N50 of 4.8 Mb and 28.6 Mb respectively. We also identified repetitive elements (accounting for 19.7% of the genome assembly) and predicted 26,905 protein-coding genes. Meanwhile, we performed genome-wide localization and characterization of several important genes encoding some key enzymes in the biosynthesis pathway of PUFAs. These genes may contribute to the high concentration of omega-3 in jade perch. Moreover, we conducted a series of comparative genomic analyses among four representative bass species at a chromosome level, resulting in a series of sequences of a deductive bass ancestor genome.
The draft genome sequence of the Brahminy blindsnake Indotyphlops braminus
Authors: Khedkar Gulab , Kambayashi Chiaki , Tabata Hiromasa , Takemura Ikuyo , Minei Ryuhei , Ogura Atsushi , Kurabayashi Atsushi 
Published: July 2022

AbstractBlindsnakes of infraoder Scolecophidia (order Squamata) are the most basal group of extant snakes, comprising of more than 450 species with ecological and morphological features highly specialized to underground living. The Brahminy blindsnake, Indotyphlops braminus, is the only known obligate parthenogenetic species of snakes. Although the origin of I. braminus is thought to be South Asia, this snake has attracted worldwide attention as an alien species, as it has been introduced to all continents except Antarctica. In this study, we present the first draft genome assembly and annotation of I. braminus. We generated approximately 480 Gbp of sequencing data and produced a draft genome with a total length of 1.86 Gbp and N50 scaffold size of 1.25 Mbp containing 89.3% of orthologs conserved in Sauropsida. We also identified 0.98 Gbp (52.82%) of repetitive genome sequences and a total of 23,560 protein-coding genes. The first draft genome of I. braminus will facilitate further study of snake evolution as well as help to understand the emergence mechanism of parthenogenetic vertebrates.
On solving the chlorine transport model via Laplace transform
Authors: Aljohani A. F. , Ebaid A. , Algehyne E. A. , Mahrous Y. M. , Agarwal P. , Areshi M. , Al-Jeaid H. K. 
Published: July 2022

AbstractThis paper analyzes the two-dimensional chlorine-transport model in pipes. The studied model is in the form of a second-order partial differential equation with a set of boundary conditions. Obtaining exact solution for the current model is a challenge due to the nature of the involved boundary conditions, especially, when applying the Laplace transform. However, such difficulties are solved via implementing the method of residues. The exact solution is obtained in terms of the Bessel functions. The expression for a dimensionless cup-mixing average concentration is also derived analytically. The proposed approach is validated via numerical examples for comparing the results with those in the literature. The present analysis/approach is effective/straightforward and can be further applied on other similar models under different boundary conditions.
Contralateral patent processus vaginalis repair in boys: a single-center retrospective study
Authors: Jinxiang Liu , Qingwei Cao , Shenghua Qiu , Yunqiang Xia , Haiyang Liu , Chengliang Liu , Meng Xu 
Published: July 2022

AbstractTo ascertain the prevalence of contralateral patent processus vaginalis (CPPV) in life and the significance of the prevalence trends for treatment. We performed a retrospective review of all inguinal hernias (IHs) that underwent repair in our hospital from 2014 to 2018. We analyzed the frequency of occurrence and treatment in boys. We assessed and compared the history, initial sides of hernia, CPPV and prognoses in different age groups. We assessed all IH cases repaired in our hospital and selected male patients of a variety of ages, including boys and men. Recurrent cases were not enrolled. A total of 3243 cases were enrolled: 2489 [right-sided IH 1411 (56.69%) vs. left-sided IH 975 (39.17%), bilateral IH 103 (4.14%)] in children and 754 [right-sided IH 485 (64.32%) vs. left-sided IH 236 (31.30%), bilateral IH 33 (4.38%)] in adults. A total of 1124 CPPVs were identified in children with unilateral IH (2386), and 12 were identified in adults (267) (p < 0.0001). There were no significant differences in recurrence rate between different subgroups of children (p > 0.05). The incidence of IH in boys was significantly higher than that in men. The number of incident cases declines rapidly with age in boys. The processus vaginalis is normally obliterated and involuted but may instead remain patent for a long period before closure; routine exploration on the contralateral side may eliminate the possibility of spontaneous PPV closure.
Uric acid and cardiometabolic risk by gender in youth with type 1 diabetes
Authors: Di Bonito Procolo , Rosanio Francesco Maria , Marcovecchio Maria Loredana , Cherubini Valentino , Delvecchio Maurizio , Di Candia Francesca , Iafusco Dario , Zanfardino Angela , Iovane Brunella , Maffeis Claudio , Maltoni Giulio , Ripoli Carlo , Piccinno Elvira , Piona Claudia Anita , Ricciardi Maria Rossella , Schiaffini Riccardo , Franzese Adriana , Mozzillo Enza 
Published: July 2022

AbstractThe aim of this study was to investigate the association between uric acid (UA) and cardiometabolic risk factors (CMRFs) by sex in youth with type 1 diabetes (T1D). Retrospective data collected from 1323 children and adolescents (5–18 years; 716 boys) with T1D recruited in 9 Italian Pediatric Diabetes Centers were analyzed. CMRFs included UA, HbA1c, blood pressure (BP), cholesterol (TC), HDL, triglycerides (TG), neutrophils (N) and lymphocytes (L) count, glomerular filtration rate (eGFR) (calculated using Schwartz-Lyon equation). In boys, we found a higher age, daily insulin dose, TG, TG/HDL ratio, TC/HDL ratio, systolic BP, N/L ratio and lower HDL, and eGFR across UA tertiles (p = 0.01–0.0001). Similar results were found in girls but not for TG and systolic BP. In boys, the odds ratio (OR) of high levels of TG/HDL ratio, TC/HDL ratio, BP and mildly reduced eGFR (MRGFR) increased for 0.5 mg/dL of UA. Instead, in girls an increased levels of 0.5 mg/dL of UA were associated with high OR of TC/HDL ratio, N/L ratio and MRGFR. Uric acid may represent a useful marker for identifying youth with T1D at high cardiometabolic risk, and this association appears to vary by sex.