bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cholangiocarcinoma combined with biliary obstruction: an exosomal circRNA signature for diagnosis and early recurrence monitoring
Authors: Wen Ningyuan , Peng Dingzhong , Xiong Xianze , Liu Geng , Nie Guilin , Wang Yaoqun , Xu Jianrong , Wang Shaofeng , Yang Sishu , Tian Yuan , Li Bei , Lu Jiong , Cheng Nansheng 
Published: May 2024

AbstractCholangiocarcinoma (CCA) is a highly malignant biliary tract cancer with currently suboptimal diagnostic and prognostic approaches. We present a novel system to monitor CCA using exosomal circular RNA (circRNA) via serum and biliary liquid biopsies. A pilot cohort consisting of patients with CCA-induced biliary obstruction (CCA-BO, n = 5) and benign biliary obstruction (BBO, n = 5) was used to identify CCA-derived exosomal circRNAs through microarray analysis. This was followed by a discovery cohort (n = 20) to further reveal a CCA-specific circRNA complex (hsa-circ-0000367, hsa-circ-0021647, and hsa-circ-0000288) in both bile and serum exosomes. In vitro and in vivo studies revealed the three circRNAs as promoters of CCA invasiveness. Diagnostic and prognostic models were established and verified by two independent cohorts (training cohort, n = 184; validation cohort, n = 105). An interpreter-free diagnostic model disclosed the diagnostic power of biliary exosomal circRNA signature (Bile-DS, AUROC = 0.947, RR = 6.05) and serum exosomal circRNA signature (Serum-DS, AUROC = 0.861, RR = 4.04) compared with conventional CA19-9 (AUROC = 0.759, RR = 2.08). A prognostic model of CCA undergoing curative-intent surgery was established by calculating early recurrence score, verified with bile samples (Bile-ERS, C-index=0.783) and serum samples (Serum-ERS, C-index = 0.782). These models, combined with other prognostic factors revealed by COX-PH model, enabled the establishment of nomograms for recurrence monitoring of CCA. Our study demonstrates that the exosomal triple-circRNA panel identified in both bile and serum samples serves as a novel diagnostic and prognostic tool for the clinical management of CCA.
Comparable outcomes for TBI-based versus treosulfan based conditioning prior to allogeneic hematopoietic stem cell transplantation in AML and MDS patients
Authors: Berning Philipp , Kolloch Lina , Reicherts Christian , Call Simon , Marx Julia , Floeth Matthias , Esseling Eva , Ronnacker Julian , Albring Jörn , Schliemann Christoph , Lenz Georg , Stelljes Matthias 
Published: May 2024

AbstractAllogeneic hematopoietic stem cell transplantation (allo-HCT) is a standard treatment for patients with AML and MDS. The combination of fractionated total body irradiation(8GyTBI/Flu) with fludarabine is an established conditioning regimen, but fludarabine/treosulfan(Flu/Treo) constitutes an alternative in older/comorbid patients. We conducted a retrospective analysis of 215 AML(in CR) and 96 MDS patients undergoing their first allo-HCT between 2011 and 2022, identifying 53 matched Flu/Treo and 8GyTBI/Flu patients through propensity score matching. Median follow-up of survivors was 3.3 years and 4.1 years. For the Flu/Treo group, 1-year non-relapse mortality (2% vs. 10%, p = 0.03) was lower, while 1-year relapse incidence (16% vs. 13%, p = 0.81) was similar. Three-year outcomes, including relapse-free survival and graft-versus-host disease incidence, were comparable (OS: 81% vs. 74%, p = 0.70; RFS: 78% vs. 66%, p = 0.28; chronic GvHD: 34% vs. 36%, p = 0.97; acute GvHD (100 days): 11% vs. 23%, p = 0.11). Multivariable analysis, considering age, ECOG, HCT-CI, and MRD status, revealed no associations with main outcomes. Dose-reduced conditioning with Flu/Treo or 8GyTBI/Flu demonstrated favorable and comparable survival rates exceeding 70% at 3 years with 1-year NRM rates below 10% and low relapse rates in the matched cohort. These data underline the need for further evaluation of TBI and Treo-based conditionings in prospective trials.
Phase stabilization of cesium lead iodide perovskites for use in efficient optoelectronic devices
Authors: Jin Handong , Zeng Yu-Jia , Steele Julian A. , Roeffaers Maarten B. J. , Hofkens Johan , Debroye Elke 
Published: May 2024

Abstract
All-inorganic lead halide perovskites (LHPs) and their use in optoelectronic devices have been widely explored because they are more thermally stable than their hybrid organic‒inorganic counterparts. However, the active perovskite phases of some inorganic LHPs are metastable at room temperature due to the critical structural tolerance factor. For example, black phase CsPbI3 is easily transformed back to the nonperovskite yellow phase at ambient temperature. Much attention has been paid to improving the phase stabilities of inorganic LHPs, especially those with high solar cell efficiencies. Herein, we discussed the origin of phase stability for CsPbI3 and the strategies used to stabilize the cubic (α) phase. We also assessed the CsPbI3 black β/γ phases that are relatively stable at nearly room temperature. Furthermore, we determined the relationship between phase stabilization and defect passivation and reviewed the growing trend in solar cell efficiency based on black phase CsPbI3. Finally, we provide perspectives for future research related to the quest for optimum device efficiency and green energy.
Cell-penetrating protein-recognizing polymeric nanoparticles through dynamic covalent chemistry and double imprinting
Authors: Ghosh Avijit , Sharma Mansi , Zhao Yan 
Published: May 2024

AbstractMolecular recognition of proteins is key to their biological functions and processes such as protein–protein interactions (PPIs). The large binding interface involved and an often relatively flat binding surface make the development of selective protein-binding materials extremely challenging. A general method is reported in this work to construct protein-binding polymeric nanoparticles from cross-linked surfactant micelles. Preparation involves first dynamic covalent chemistry that encodes signature surface lysines on a protein template. A double molecular imprinting procedure fixes the binding groups on the nanoparticle for these lysine groups, meanwhile creating a binding interface complementary to the protein in size, shape, and distribution of acidic groups on the surface. These water-soluble nanoparticles possess excellent specificities for target proteins and sufficient affinities to inhibit natural PPIs such as those between cytochrome c (Cytc) and cytochrome c oxidase (CcO). With the ability to enter cells through a combination of energy-dependent and -independent pathways, they intervene apoptosis by inhibiting the PPI between Cytc and the apoptotic protease activating factor-1 (APAF1). Generality of the preparation and the excellent molecular recognition of the materials have the potential to make them powerful tools to probe protein functions in vitro and in cellulo.
Genetic and phenotypic characterization of Parkinson’s disease at the clinic-wide level
Authors: Tropea Thomas F. , Hartstone Whitney , Amari Noor , Baum Dylan , Rick Jacqueline , Suh Eunran , Zhang Hanwen , Paul Rachel A. , Han Noah , Zack Rebecca , Brody Eliza M. , Albuja Isabela , James Justin , Spindler Meredith , Deik Andres , Aamodt Whitley W. , Dahodwala Nabila , Hamedani Ali , Lasker Aaron , Hurtig Howard , Stern Matthew , Weintraub Daniel , Vaswani Pavan , Willis Allison W. , Siderowf Andrew , Xie Sharon X. , Van Deerlin Vivianna , Chen-Plotkin Alice S. 
Published: May 2024

AbstractObservational studies in Parkinson’s disease (PD) deeply characterize relatively small numbers of participants. The Molecular Integration in Neurological Diagnosis Initiative seeks to characterize molecular and clinical features of every PD patient at the University of Pennsylvania (UPenn). The objectives of this study are to determine the feasibility of genetic characterization in PD and assess clinical features by sex and GBA1/LRRK2 status on a clinic-wide scale. All PD patients with clinical visits at the UPenn PD Center between 9/2018 and 12/2022 were eligible. Blood or saliva were collected, and a clinical questionnaire administered. Genotyping at 14 GBA1 and 8 LRRK2 variants was performed. PD symptoms were compared by sex and gene groups. 2063 patients were approached and 1,689 (82%) were enrolled, with 374 (18%) declining to participate. 608 (36%) females were enrolled, 159 (9%) carried a GBA1 variant, and 44 (3%) carried a LRRK2 variant. Compared with males, females across gene groups more frequently reported dystonia (53% vs 46%, p = 0.01) and anxiety (64% vs 55%, p < 0.01), but less frequently reported cognitive impairment (10% vs 49%, p < 0.01) and vivid dreaming (53% vs 60%, p = 0.01). GBA1 variant carriers more frequently reported anxiety (67% vs 57%, p = 0.04) and depression (62% vs 46%, p < 0.01) than non-carriers; LRRK2 variant carriers did not differ from non-carriers. We report feasibility for near-clinic-wide enrollment and characterization of individuals with PD during clinical visits at a high-volume academic center. Clinical symptoms differ by sex and GBA1, but not LRRK2, status.
Decellularised plant scaffolds facilitate porcine skeletal muscle tissue engineering for cultivated meat biomanufacturing
Authors: Murugan Priyatharshini , Yap Wee Swan , Ezhilarasu Hariharan , Suntornnond Ratima , Le Quang Bach , Singh Satnam , Seah Jasmine Si Han , Tan Pei Leng , Zhou Weibiao , Tan Lay Poh , Choudhury Deepak 
Published: May 2024

AbstractCultivated meat (CM) offers a sustainable and ethical alternative to conventional animal agriculture, involving cell maturation in a controlled environment. To emulate the structural complexity of traditional meat, the development of animal-free and edible scaffolds is crucial, providing vital physical and biological support during tissue development. The aligned vascular bundles of the decellularised asparagus scaffold were selected to facilitate the attachment and alignment of murine myoblasts (C2C12) and porcine adipose-derived mesenchymal stem cells (pADMSCs). Muscle differentiation was assessed through immunofluorescence staining with muscle markers, including Myosin heavy chain (MHC), Myogenin (MYOG), and Desmin. The metabolic activity of Creatine Kinase in C2C12 differentiated cells significantly increased compared to proliferated cells. Quantitative PCR analysis revealed a significant increase in Myosin Heavy Polypeptide 1 (MYH1) and MYOG expression compared to Day 0. These results highlight the application of decellularised plant scaffold (DPS) as a promising, edible material conducive to cell attachment, proliferation, and differentiation into muscle tissue. To create a CM prototype with biological mimicry, pADMSC-derived muscle and fat cells were also co-cultured on the same scaffold. The co-culture was confirmed through immunofluorescence staining of muscle markers and LipidTOX staining, revealing distinct muscle fibres and adipocytes containing lipid droplets respectively. Texture profile analysis conducted on uncooked CM prototypes and pork loin showed no significant differences in textural values. However, the pan-fried CM prototype differed significantly in hardness and chewiness compared to pork loin. Understanding the scaffolds’ textural profile enhances our insight into the potential sensory attributes of CM products. DPS shows potential for advancing CM biomanufacturing.
Designing function-specific minimal microbiomes from large microbial communities
Authors: Raghu Aswathy K. , Palanikumar Indumathi , Raman Karthik 
Published: May 2024

AbstractMicroorganisms exist in large communities of diverse species, exhibiting various functionalities. The mammalian gut microbiome, for instance, has the functionality of digesting dietary fibre and producing different short-chain fatty acids. Not all microbes present in a community contribute to a given functionality; it is possible to find a minimal microbiome, which is a subset of the large microbiome, that is capable of performing the functionality while maintaining other community properties such as growth rate and metabolite production. Such a minimal microbiome will also contain keystone species for SCFA production in that community. In this work, we present a systematic constraint-based approach to identify a minimal microbiome from a large community for a user-proposed function. We employ a top-down approach with sequential deletion followed by solving a mixed-integer linear programming problem with the objective of minimising the L1-norm of the membership vector. Notably, we consider quantitative measures of community growth rate and metabolite production rates. We demonstrate the utility of our algorithm by identifying the minimal microbiomes corresponding to three model communities of the gut, and discuss their validity based on the presence of the keystone species in the community. Our approach is generic, flexible and finds application in studying a variety of microbial communities. The algorithm is available from https://github.com/RamanLab/minMicrobiome.
Selection of a promiscuous minimalist cAMP phosphodiesterase from a library of de novo designed proteins
Authors: Schnettler J. David , Wang Michael S. , Gantz Maximilian , Bunzel H. Adrian , Karas Christina , Hollfelder Florian , Hecht Michael H. 
Published: May 2024

AbstractThe ability of unevolved amino acid sequences to become biological catalysts was key to the emergence of life on Earth. However, billions of years of evolution separate complex modern enzymes from their simpler early ancestors. To probe how unevolved sequences can develop new functions, we use ultrahigh-throughput droplet microfluidics to screen for phosphoesterase activity amidst a library of more than one million sequences based on a de novo designed 4-helix bundle. Characterization of hits revealed that acquisition of function involved a large jump in sequence space enriching for truncations that removed >40% of the protein chain. Biophysical characterization of a catalytically active truncated protein revealed that it dimerizes into an α-helical structure, with the gain of function accompanied by increased structural dynamics. The identified phosphodiesterase is a manganese-dependent metalloenzyme that hydrolyses a range of phosphodiesters. It is most active towards cyclic AMP, with a rate acceleration of ~109 and a catalytic proficiency of >1014 M−1, comparable to larger enzymes shaped by billions of years of evolution.
Chromosome-level genome assembly of the threatened resource plant Cinnamomum chago
Authors: Tao Lidan , Guo Shiwei , Xiong Zizhu , Zhang Rengang , Sun Weibang 
Published: May 2024

AbstractCinnamomum chago is a tree species endemic to Yunnan province, China, with potential economic value, phylogenetic importance, and conservation priority. We assembled the genome of C. chago using multiple sequencing technologies, resulting in a high-quality, chromosomal-level genome with annotation information. The assembled genome size is approximately 1.06 Gb, with a contig N50 length of 92.10 Mb. About 99.92% of the assembled sequences could be anchored to 12 pseudo-chromosomes, with only one gap, and 63.73% of the assembled genome consists of repeat sequences. In total, 30,497 genes were recognized according to annotation, including 28,681 protein-coding genes. This high-quality chromosome-level assembly and annotation of C. chago will assist us in the conservation and utilization of this valuable resource, while also providing crucial data for studying the evolutionary relationships within the Cinnamomum genus, offering opportunities for further research and exploration of its diverse applications.
A dataset for measuring the impact of research data and their curation
Authors: Hemphill Libby , Thomer Andrea , Lafia Sara , Fan Lizhou , Bleckley David , Moss Elizabeth 
Published: May 2024

AbstractScience funders, publishers, and data archives make decisions about how to responsibly allocate resources to maximize the reuse potential of research data. This paper introduces a dataset developed to measure the impact of archival and data curation decisions on data reuse. The dataset describes 10,605 social science research datasets, their curation histories, and reuse contexts in 94,755 publications that cover 59 years from 1963 to 2022. The dataset was constructed from study-level metadata, citing publications, and curation records available through the Inter-university Consortium for Political and Social Research (ICPSR) at the University of Michigan. The dataset includes information about study-level attributes (e.g., PIs, funders, subject terms); usage statistics (e.g., downloads, citations); archiving decisions (e.g., curation activities, data transformations); and bibliometric attributes (e.g., journals, authors) for citing publications. This dataset provides information on factors that contribute to long-term data reuse, which can inform the design of effective evidence-based recommendations to support high-impact research data curation decisions.
Feasibility, safety, efficacy and potential scaling-up of sofosbuvir-based HCV treatment in Central and West Africa: (TAC ANRS 12311 trial)
Authors: Lacombe Karine , Moh Raoul , Chazallon Corine , Lemoine Maud , Sylla Babacar , Fadiga Fatoumata , Le Carrou Jerôme , Marcellin Fabienne , Kouanfack Charles , Ciaffi Laura , Sartre Michelle Tagni , Sida Magloire Biwole , Diallo Alpha , Gozlan Joel , Seydi Moussa , Cissé Viviane , Danel Christine , Girard Pierre Marie , Toni Thomas d’Aquin , Minga Albert , Boyer Sylvie , Carrieri Patrizia , Attia Alain ,   The TAC ANRS12311 Study Group, Karcher Sophie , Touret Pierre , Mory Camara , Lawson-Ananissoh Laté Mawuli , Konan Romuald , Lakhe Ndèye Aissatou , Fall Batsy Koita , N’Diaye Bara , Toure Kane Coumba , Tagni-Sartre Michelle , Dang Babagna Isabelle , Tchoumi Eric Pascal , Mpoundi Ngole Eitel , Aghokeng Avelin , Djubgang Rina 
Published: May 2024

AbstractAccess to Hepatis C treatment in Sub-Saharan Africa is a clinical, public health and ethical concern. The multi-country open-label trial TAC ANRS 12311 allowed assessing the feasibility, safety, efficacy of a specific care model of HCV treatment and retreatment in patients with hepatitis C in Sub Saharan Africa. Between November 2015 and March 2017, with follow-up until mid 2019, treatment-naïve patients with HCV without decompensated cirrhosis or liver cancer were recruited to receive 12 week-treatment with either sofosbuvir + ribavirin (HCV genotype 2) or sofosbuvir + ledipasvir (genotype 1 or 4) and retreatment with sofosbuvir + velpatasvir + voxilaprevir in case of virological failure. The primary outcome was sustained virological response at 12 weeks after end of treatment (SVR12). Secondary outcomes included treatment adherence, safety and SVR12 in patients who were retreated due to non-response to first-line treatment. The model of care relied on both viral load assessment and educational sessions to increase patient awareness, adherence and health literacy. The study recruited 120 participants, 36 HIV-co-infected, and 14 cirrhotic. Only one patient discontinued treatment because of return to home country. Neither death nor severe adverse event occurred. SVR12 was reached in 107 patients (89%): (90%) in genotype 1 or 2, and 88% in GT-4. All retreated patients (n = 13) reached SVR12. HCV treatment is highly acceptable, safe and effective under this model of care. Implementation research is now needed to scale up point-of-care HCV testing and SVR assessment, along with community involvement in patient education, to achieve HCV elimination in Sub-Saharan Africa.
Enhancing soccer goalkeepers penalty dive kinematics with instructional video and laterality insights in field conditions
Authors: Monteiro Rafael Luiz Martins , dos Santos Carlos Cesar Arruda , Blauberger Patrick , Link Daniel , Russomanno Tiago Guedes , Tahara Ariany Klein , Chinaglia Abel Gonçalves , Santiago Paulo Roberto Pereira 
Published: May 2024

AbstractThis study aimed to analyze the effect of laterality and instructional video on the soccer goalkeepers’ dive kinematics in penalty. Eight goalkeepers from youth categories (U15, U17, U20) were randomly divided into control (CG) and video instruction groups (VG). The latter performed 20 penalty defense trials on the field with balls launched by a machine, ten before and after watching a video instruction to improve the diving kinematics. The CG only performed the dives. Three cameras recorded the collections. A markerless motion capture technique (OpenPose) was used for identification and tracking of joints and anatomical references on video. The pose data were used for 3D reconstruction. In the post-instruction situation, the VG presented differences in comparison to the CG in the: knee flexion/extension angle, time to reach peak resultant velocity, frontal step distance, and frontal departure angle, which generated greater acceleration during the dive. Non-dominant leg side dives had higher resultant velocity during 88.4 – 100% of the diving cycle, different knee flexion/extension angle, and higher values ​​in the frontal step distance. The instructional video generated an acute change in the diving movement pattern of young goalkeepers when comparing the control and the video instruction group in the post condition.
Four-years change of BMI and waist circumference are associated with metabolic syndrome in middle-aged and elderly Chinese
Authors: Zhang Xiaoyun , Wang Ying , Li Yuqing , Gui Jiaofeng , Mei Yujin , Yang Xue , Liu Haiyang , Guo Lei-lei , Li Jinlong , Lei Yunxiao , Li Xiaoping , Sun Lu , Yang Liu , Yuan Ting , Wang Congzhi , Zhang Dongmei , Li Jing , Liu Mingming , Hua Ying , Zhang Lin 
Published: May 2024

AbstractThe purpose of the study was to determine whether changes in body mass index (BMI) and waist circumference (WC) in middle-aged and elderly Chinese are associated with metabolic syndrome. In this cohort investigation, 3697 middle-aged and elderly people aged 45 or over were recruited from the China Health and Retirement Longitudinal Study (CHARLS). The National Cholesterol Education Program Adult Treatment Panel III (2005) defined metabolic syndrome (MetS). With Cox regression analysis, we calculated hazard ratio (HR) and 95% confidence intervals (CIs) for MetS based on BMI-WC change categories. To assess the prevalence of MetS, the changes in BMI and WC levels were classified into four quartiles based on their relative and absolute changes. In subjects whose BMI and WC decreased (HR = 0.338; 95% CIs 0.264, 0.433) as well as those whose BMI increased and their WC decreased (HR = 0.375; 95% CIs 0.228, 0.499), metabolic syndrome risk was significantly lower compared with those with increases in both BMI and WC. Regarding the absolute changes in BMI, the lowest percentile of BMI was significantly lower in both males (HR = 0.302; 95% CIs 0.204, 0.448) and females (HR = 0.486; 95% CIs 0.354, 0.667) for the risk of metabolic syndrome. Similar results were observed in the absolute changes in WC, with the lowest quantile of WC having a significant impact on MetS risk in males (HR = 0.170; 95% CIs 0.107, 0.270) and females (HR = 0.303; 95% CIs 0.217, 0.424). The risk of metabolic syndrome was significantly associated with changes in BMI and WC in middle-aged and elderly Chinese. A reduced BMI and WC are associated with lower metabolic syndrome risks in middle-aged and elderly people.