bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pedigree genome data of an early-matured Geng/japonica glutinous rice mega variety Longgeng 57
Authors: Lei Yuanbao , Zhang Yunjiang , Xu Linyun , Ma Wendong , Zhou Ziqi , Li Jie , Quan Pengyu , Faruquee Muhiuddin , Yang Dechen , Zhang Fan , Zhou Yongli , Quan Guangjun , Zhao Xiuqin , Wang Wensheng , Liu Bailong , Li Zhikang , Xu Jianlong , Zheng Tianqing 
Published: February 2024

AbstractBy using PacBio HiFi technology, we produced over 700 Gb of long-read sequencing (LRS) raw data; and by using Illumina paired-end whole-genome shotgun (WGS) sequencing technology, we generated more than 70 Gb of short-read sequencing (SRS) data. With LRS data, we assembled one genome and then generate a set of annotation data for an early-matured Geng/japonica glutinous rice mega variety genome, Longgeng 57 (LG57), which carries multiple elite traits including good grain quality and wide adaptability. Together with the SRS data from three parents of LG57, pedigree genome variations were called for three representative types of genes. These data sets can be used for deep variation mining, aid in the discovery of new insights into genome structure, function, and evolution, and help to provide essential support to biological research in general.
ReTimeML: a retention time predictor that supports the LC–MS/MS analysis of sphingolipids
Authors: Allwright Michael , Guennewig Boris , Hoffmann Anna E. , Rohleder Cathrin , Jieu Beverly , Chung Long H. , Jiang Yingxin C. , Lemos Wimmer Bruno F. , Qi Yanfei , Don Anthony S. , Leweke F. Markus , Couttas Timothy A. 
Published: February 2024

AbstractThe analysis of ceramide (Cer) and sphingomyelin (SM) lipid species using liquid chromatography–tandem mass spectrometry (LC–MS/MS) continues to present challenges as their precursor mass and fragmentation can correspond to multiple molecular arrangements. To address this constraint, we developed ReTimeML, a freeware that automates the expected retention times (RTs) for Cer and SM lipid profiles from complex chromatograms. ReTimeML works on the principle that LC–MS/MS experiments have pre-determined RTs from internal standards, calibrators or quality controls used throughout the analysis. Employed as reference RTs, ReTimeML subsequently extrapolates the RTs of unknowns using its machine-learned regression library of mass-to-charge (m/z) versus RT profiles, which does not require model retraining for adaptability on different LC–MS/MS pipelines. We validated ReTimeML RT estimations for various Cer and SM structures across different biologicals, tissues and LC–MS/MS setups, exhibiting a mean variance between 0.23 and 2.43% compared to user annotations. ReTimeML also aided the disambiguation of SM identities from isobar distributions in paired serum-cerebrospinal fluid from healthy volunteers, allowing us to identify a series of non-canonical SMs associated between the two biofluids comprised of a polyunsaturated structure that confers increased stability against catabolic clearance.
Differential sedimentary evolution of typical aulacogens of Meso-Neoproterozoic in North China craton
Authors: Tan Cong , Lyu Qiqi , Wang Tongshan , Li Qiufen , Jiang Hua , Yan Xue 
Published: February 2024

AbstractMany countries and regions in the world have obtained industrial oil flow in the Meso-Neoproterozoic sedimentary strata and formed commercial exploitation in recent years. The development horizon of high-quality source rocks in the Proterozoic in North China can be compared with the international, indicating that the Meso-Neoproterozoic in North China has great exploration potential. The sedimentary characteristics of typical aulacogen in multiple cratons in the Meso-Neoproterozoic North China Craton are compared and studied by using field outcrop data, drilling data and analysis and test data, aiming to provide sedimentary support for the prediction of oil and gas distribution and evaluation of exploration field in the Meso-Neoproterozoic in this area. The results show that there are four sedimentary systems in the study area, including Marine clastic rock sedimentary system, Marine carbonate sedimentary system, Marine-continental transitional facies sedimentary system and glacial sedimentary system. They are divided into seven sedimentary facies types: barrier coastal facies, non-barrier coast facies, shallow shelf facies, carbonate platform facies, reef facies, fan delta facies and glacial facies, and further divided into 15 subfacies and 21 microfacies. On this basis, the Meso-Neoproterozoic sedimentary filling sequences of two typical aulacogens, Yanliao and Xiong 'er, in the study area are clarified, showing that the formation time of each sedimentary filling sequence stage of different aulacogens is different, and the rock characteristics, lithology combination, lithologic structure, contact relationship, vertical sequence and sedimentary facies assemblage of the same sedimentary filling sequence stage are obviously different. The filling characteristics of the two aulacogens completely record the geological events related to the breakup of the Colombian supercontinent.
Multiparametric in vitro and in vivo analysis of the safety profile of self-assembling peptides
Authors: Ramirez-Labrada Ariel , Santiago Llipsy , Pesini Cecilia , Arrieta Marta , Arias Maykel , Calvo Pérez Adanays , Ciulla Maria Gessica , Forouharshad Mahdi , Pardo Julian , Gálvez Eva M. , Gelain Fabrizio 
Published: February 2024

AbstractSelf-assembling peptides (SAPs) have gained significant attention in biomedicine because of their unique properties and ability to undergo molecular self-assembly driven by non-covalent interactions. By manipulating their composition and structure, SAPs can form well-ordered nanostructures with enhanced selectivity, stability and biocompatibility. SAPs offer advantages such as high chemical and biological diversity and the potential for functionalization. However, studies concerning its potentially toxic effects are very scarce, a limitation that compromises its potential translation to humans. This study investigates the potentially toxic effects of six different SAP formulations composed of natural amino acids designed for nervous tissue engineering and amenable to ready cross-linking boosting their biomechanical properties. All methods were performed in accordance with the relevant guidelines and regulations. A wound-healing assay was performed to evaluate how SAPs modify cell migration. The results in vitro demonstrated that SAPs did not induce genotoxicity neither skin sensitization. In vivo, SAPs were well-tolerated without any signs of acute systemic toxicity. Interestingly, SAPs were found to promote the migration of endothelial, macrophage, fibroblast, and neuronal-like cells in vitro, supporting a high potential for tissue regeneration. These findings contribute to the development and translation of SAP-based biomaterials for biomedical applications.
Competing risk multistate censored data modeling by propensity score matching method
Authors: Bhattacharjee Atanu , Vishwakarma Gajendra K. , Tripathy Abhipsa , Rajbongshi Bhrigu Kumar 
Published: February 2024

AbstractThe potential contribution of the paper is the use of the propensity score matching method for updating censored observations within the context of multi-state model featuring two competing risks.The competing risks are modelled using cause-specific Cox proportional hazard model.The simulation findings demonstrate that updating censored observations tends to lead to reduced bias and mean squared error for all estimated parameters in the risk of cause-specific Cox model.The results for a chemoradiotherapy real dataset are consistent with the simulation results.
α-lipoic acid modulates prostate cancer cell growth and bone cell differentiation
Authors: Abdullah K. M. , Sharma Gunjan , Takkar Simran , Kaushal Jyoti B. , Pothuraju Ramesh , Chakravarti Bandana , Batra Surinder K. , Siddiqui Jawed A. 
Published: February 2024

AbstractProstate cancer (PCa) progression leads to bone modulation in approximately 70% of affected men. A nutraceutical, namely, α-lipoic acid (α-LA), is known for its potent anti-cancer properties towards various cancers and has been implicated in treating and promoting bone health. Our study aimed to explore the molecular mechanism behind the role of α-LA as therapeutics in preventing PCa and its associated bone modulation. Notably, α-LA treatment significantly reduced the cell viability, migration, and invasion of PCa cell lines in a dose-dependent manner. In addition, α-LA supplementation dramatically increased reactive oxygen species (ROS) levels and HIF-1α expression, which started the downstream molecular cascade and activated JNK/caspase-3 signaling pathway. Flow cytometry data revealed the arrest of the cell cycle in the S-phase, which has led to apoptosis of PCa cells. Furthermore, the results of ALP (Alkaline phosphatase) and TRAP (tartrate-resistant acid phosphatase) staining signifies that α-LA supplementation diminished the PCa-mediated differentiation of osteoblasts and osteoclasts, respectively, in the MC3T3-E1 and bone marrow macrophages (BMMs) cells. In summary, α-LA supplementation enhanced cellular apoptosis via increased ROS levels, HIF-1α expression, and JNK/caspase-3 signaling pathway in advanced human PCa cell lines. Also, the treatment of α-LA improved bone health by reducing PCa-mediated bone cell modulation.
MicroRNA expression and oxidative stress markers in pectoral muscle of broiler chickens fed diets supplemented with phytobiotics composition
Authors: Chodkowska Karolina A. , Barszcz Marcin , Tuśnio Anna 
Published: February 2024

AbstractPhytobiotic compositions are commercially used in broiler production, mostly to improve general health and the production parameters. Moreover, some of their active substances may change the expression of miRNA in different tissues. Therefore, the purpose of this study was to evaluate the effect of the phytobiotic composition (PBC) containing white mustard, calamus, turmeric, and common ivy on production parameters, oxidative stress markers and expression of selected miRNAs in pectoral muscle of broiler chickens. The experiment was performed on broiler chickens fed the control diet (without PBC), and a diet supplemented with 60 or 100 mg/kg of PBC for 35 days. After the experiment, samples (blood and muscle) were collected for analyses. The analyzed production parameters included: feed conversion ratio, feed intake and body weight. There was no effect on growth performance of broiler chickens but feeding diet supplemented with 60 mg/kg phytobiotics significantly increased the expression of miR-30a-5p, miR-181a-5p, and miR-206, and decreased that of miR-99a-5p, miR-133a-5p, miR-142-5p, and miR-222 in pectoral muscle of chickens. The addition of 100 mg/kg phytobiotics significantly increased miR-99a-5p and miR-181a-5p expression, and caused down-regulation of the expression of miR-26a-5p and miR-30a-5p. Chickens fed diet supplemented with 100 mg/kg PBC had lower level of lipid peroxidation products in blood, while in the muscle tissue it was higher in birds fed a diet with the addition of 60 mg/kg as compared to the control group. The results suggest that this unique composition of phytobiotics does not affect productive traits but can change expression of miRNAs that are crucial for muscle physiology and pathology in broiler chickens. This additive may also protect against the oxidative stress but the effect is dose dependent.
A validation study of the Occupational Depression Inventory in Poland and Ukraine
Authors: Golonka Krystyna , Malysheva Karine O. , Fortuna Dominika , Gulla Bożena , Lytvyn Serhii , De Beer Leon T. , Schonfeld Irvin Sam , Bianchi Renzo 
Published: February 2024

AbstractThis study examined the psychometric and structural properties of the Polish and Ukrainian versions of the Occupational Depression Inventory (ODI). We relied on two samples of Polish employees (NSample1 = 526, 47% female; NSample2 = 164, 64% female) and one sample of Ukrainian employees (NSample3 = 372, 73% female). In all samples, the ODI exhibited essential unidimensionality and high total-score reliability (e.g., McDonald’s omegas > 0.90). The homogeneity of the scale was strong (e.g., 0.59 ≤ scale-level Hs ≤ 0.68). The ODI’s total scores thus accurately ranked individuals on a latent occupational depression continuum. We found evidence of complete measurement invariance across our samples, a prerequisite for between-group comparisons involving observed scores. Looking into the criterion validity of the ODI, we found occupational depression to correlate, in the expected direction, with resilience and job-person fit in six areas of working life—workload, control, rewards, community, fairness, and values. The prevalence of occupational depression was estimated at 5% in Sample 1, 18% in Sample 2, and 3% in Sample 3. Our findings support the use of the ODI’s Polish and Ukrainian versions. This study adds to a growing corpus of research suggesting that the ODI is a robust instrument.
Mikrobiom: von der Pathophysiologie in die Klinik?
Authors: Scharl Michael , Rogler Gerhard 
Published: February 2024

Zusammenfassung
WAS IST NEU?

Die fest etablierte Indikation der Mikrobiota-Therapie:
Clostridioides-difficile-Infektion
Die fäkale Mikrobiota-Transplantation (FMT,
„Stuhltransplantation“) ist sehr effektiv zur Behandlung der
rezidivierenden Clostridioides-difficile-Diarrhöe. Sie ist nun nach den
nationalen und internationalen Leitlinien spätestens beim zweiten
Rezidiv indiziert. Erste kommerziell hergestellte FMT-Produkte (Rebyota) sind
bereits in den USA zugelassen und bei uns im Zulassungsprozess.
Kapsel-Präparate aus gereinigten Clostridien-Sporen haben bei der
Clostridioides-difficile-Diarrhöe positive Ergebnisse gezeigt und sind
ebenfalls im Prozess der Zulassung.
Mikrobiom und Reizdarmsyndrom
Beim Reizdarmsyndrom sind die Studien zur FMT teilweise widersprüchlich.
Der Verabreichungsweg (Duodenalsonde oder Koloskopie) spielt
möglicherweise eine Rolle.
FMT bei chronisch-entzündlichen Darmerkrankungen
Bei chronisch-entzündlichen Darmerkrankungen verfestigen sich die Belege,
dass FMT bei Colitis ulcerosa wirksam ist, beim Morbus Crohn jedoch nicht.
Das Mikrobiom bei onkologischen Erkrankungen
In der Onkologie verfestigen sich Befunde, dass die Mikrobiota die Immunantwort
gegen Tumoren und Metastasen beeinflussen kann. Erste Studien zeigen, dass bei
manchen Non-Respondern gegenüber einer Checkpoint-Inhibitor-Therapie die
Therapieantwort durch FMT von einem Spender mit gutem Therapieresponse
wiederhergestellt werden kann.
Der MEDPass-Verabreichungsmodus oraler Nahrungssupplemente –
vom Entscheid bis zur Nachbetreuung
Authors: Kaufmann Anita , Uhlmann Katja , Kurmann Silvia 
Published: February 2024

Zusammenfassung
Einleitung Orale Nahrungssupplemente können alternativ zur
nicht-standardisierten Verabreichung im sogenannten MEDPass Verabreichungsmodus
in unüblich kleinen Mengen zusammen mit den Medikamentenrunden serviert
werden. Studien zum MEDPass deuten auf eine verbesserte Einnahmeadhärenz
hin. Empfehlungen von Fachgesellschaften für den Einsatz des MEDPass
existieren keine. Wie weit sich der MEDPass in Deutschschweizer
Spitälern und Rehabilitationskliniken etabliert hat und welche
Professionen in welche Prozessschritte involviert sind, ist unbekannt. In dieser
Studie wurde diesen Fragestellungen nachgegangen.
Methodik In Deutschschweizer Spitälern und Rehabilitationskliniken
wurde von März bis April 2022 eine online-Umfrage durchgeführt
und deskriptiv ausgewertet. Pro Institution nahm stellvertretend ein*e
Ernährungsberater*in teil und beantwortete bis zu sechs Fragen
zur Etablierung und bis zu 14 Fragen zu den Prozessschritten des MEDPass.
Ergebnisse Die Rücklaufquote betrug 71.4% (n=80).
Der MEDPass ist in 68.5% (n=50) der Institutionen etabliert.
Ernährungsberater*innen bestimmen den Verabreichungsmodus, die
Dosierung, die Verordnung sowie die Fortführung der Einnahme nach dem
Austritt. Pflegefachpersonen sind für die Verabreichung, die Motivation
der Patient*innen, die Überwachung der Einnahmeadhärenz
und für die Dokumentation der Einnahme zuständig. Im
Austrittsmanagement übernehmen die
Ernährungsberater*innen die Organisation der Kostengutsprache
und die Bestellung der oralen Nahrungssupplemente. In 38.3%
(n=18) der Institutionen werden die Patient*innen
ernährungstherapeutisch nachbetreut.
Schlussfolgerungen Der MEDPass ist trotz fehlender Empfehlung weit
verbreitet. Die Verordnungspraxis weicht von der rechtlichen Situation ab und
ist in der Schweiz weiter in Diskussion. Da die Prozessschritte mehrheitlich
klar den Professionen zugewiesen wurden, können die Resultate als
Wegweiser für die MEDPass Einführung dienen.
The Continued Impact of Godina's Principles: Outcomes of Flap Coverage as a Function of Time After Definitive Fixation of Open Lower Extremity Fractures
Authors: Le Elliot L. H. , McNamara Colin T. , Constantine Ryan S. , Greyson Mark A. , Iorio Matthew L. 
Published: February 2024

Abstract
Background Early soft tissue coverage of open lower extremity fractures within 72 hours of injury leads to improved outcomes. Little is known about outcomes when definitive fixation is completed first. The purpose of this study is to quantify postoperative outcomes when soft tissue reconstruction is delayed until after definitive open reduction and internal fixation (ORIF) is completed.
Methods An insurance claims database was queried for all patients with open lower extremity fractures between 2010 and 2020 who underwent free or axial flap reconstruction after ORIF. This cohort was stratified into three groups: reconstruction performed 0 to 3, 3 to 7, and 7+ days after ORIF. The primary outcome was 90-day complication and reoperation rates. Bivariate and multivariable regression of all-cause complications and reoperations was evaluated for time to flap as a risk factor.
Results A total of 863 patients with open lower extremity fractures underwent ORIF prior to flap soft tissue reconstruction. In total, 145 (16.8%), 162 (18.8%), and 556 (64.4%) patients underwent soft tissue reconstruction 0 to 3 days, 4 to 7 days, and 7+ days after ORIF, respectively. The 90-day complication rate of surgical site infections ( SSI; 16.6%, 16,7%, 28.8%; p = 0.001) and acute osteomyelitis (5.5%, 6.2%, 27.7%; p < 0.001) increased with delayed soft tissue reconstruction. Irrigation and debridement rates were directly related to time from ORIF to flap (33.8%, 51.9%, 61.9%; p < 0.001). Hardware removal rates were significantly higher with delayed treatment (10.3%, 9.3%, 39.3%; p < 0.001). The 0 to 3 day (odds ratio [OR] = 0.22; 95% confidence interval [CI]: 0.15, 0.32) and 4 to 7 day (OR = 0.26; 95% CI: 0.17, 0.40) groups showed protective factors against all-cause complications after bivariate and multivariate regression.
Conclusion Early soft tissue reconstruction of open lower extremity fractures performed within 7 days of ORIF reduces complication rates and reduces the variability of complication rates including SSIs, acute osteomyelitis, and hardware failure.
Intimal Hemorrhage of Basilar Artery Induced by Severe Vasospasm Following Subarachnoid Hemorrhage: The Experimental Analysis
Authors: Gökyar Ahmet , Şahin Mehmet Hakan , Karadağ Mehmet Kürşat , Bahadır Sinan , Zeynal Mete , Sipal Sare Altas , Aydin Mehmet D. 
Published: February 2024

Abstract
Background Cerebral vasospasm, a serious complication of subarachnoid hemorrhage (SAH), has been extensively studied for its neurochemical and pathophysiologic mechanisms. However, the contribution of inner elastic membrane dissection and subintimal hemorrhage to basilar artery occlusion remains underexplored. This study investigates inner elastic membrane-related changes in the basilar artery after SAH.
Methods Twenty-four hybrid rabbits were divided into control, sham, and SAH groups, with SAH induced by autologous blood injection. After 2 weeks, basilar artery changes, vasospasm indexes (VSIs), and dissections were evaluated.
Results The SAH group showed significantly higher VSI, with vascular wall thickening, luminal narrowing, convoluted smooth muscle cells, intimal elastic membrane disruption, endothelial cell desquamation, and apoptosis. Some SAH animals exhibited subintimal hemorrhage, inner elastic membrane dissection, and ruptures. Basilar arteries with subintimal hemorrhage had notably higher VSI.
Conclusions These findings highlight the role of subintimal hemorrhage and inner elastic membrane dissection in basilar artery occlusion post-SAH, offering valuable insights into vasospasm pathophysiology.
Biomechanical Analysis of Mandibular Premolar Restored with Different Custom Post Core
Authors: Gavranović-Glamoč Alma , Jakupović Selma , Cerjaković Edin , Topčić Alan , Berhamović Emir , Kazazić Lejla , Strujić-Porović Sanela , Šehić Adnan , Bajrić Elmedin 
Published: February 2024

Abstract
Objective This study investigated biomechanical behavior of custom post core made of six different materials on the tooth with and without the ferrule under different occlusal load.
Materials and Methods Three-dimensional models of mandibular first premolar, with and without ferrule, reconstructed from micro-computed tomography image are restored with different custom post core and zirconia crowns. By using the finite element analysis, von Mises stress shown in MPa was measured under simulated axial and oblique load of 200 [N]. To compare the stress distribution, six different custom post core materials were chosen: zirconia, Ni-Cr alloy, gold alloy, glass fiber-polyether ether ketone, polyether ether ketone, and carbon fiber-polyether ether ketone.
Results Custom post cores with a higher modulus of elasticity showed higher measured stress in the posts, but less stress in dentin. Measured stress in custom post core under oblique loading was approximately three times higher compared with axial loading. Stress in custom post core and in dentin under both types of loads was slightly higher in teeth without ferrule effect.
Conclusion The use of custom cast post cores made of different alloys is recommended in restoration of endodontically treated teeth, with extensive loss of tooth structure especially in teeth without ferrule effect.