bluuebunny/crossref_metadata_2025_split huggingface dataset:
A semi-balanced section in the northwestern Zagros region: Constraining the structural architecture of the Mountain Front Flexure in the Kirkuk Embayment, Iraq
Authors: Hinsch Ralph , Bretis Bernhard 
Published: October 2021

ABSTRACT
The Mountain Front Flexure or Fault (MFF) of the Zagros Mountains separates the foreland or foothills area from the morphological apparent mountain belt. Across this feature the regional elevations of Mesozoic to Neogene stratigraphic horizons substantially rise towards the mountain belt. Thin-skinned and thick-skinned structural styles have been proposed for this rise in other parts of the Zagros region. In our study area, in the Kurdistan Region of Iraq (KRI), we integrated surface and subsurface data and constructed a (semi-) balanced cross-section across the MFF. The section features duplex structures in the deeper subsurface, related to a deeper Palaeozoic and a shallower Triassic decollement horizon. On a smaller scale, layer-parallel shortening and intense deformation is observed in the incompetent lithologies, leading to an incipient disharmonic folding. Restoration of the section reveals a distinct imbalance between shortening in the upper part of the stratigraphic section (approximately 4 km or 16% on top Jurassic level) to the lower part (approximately 20 km or 49% on top Permian level). The imbalance can only be equalised on a regional section if the shortening is transferred from the lower to the higher decollement levels, which is connected to folds and thrusts in the foothills area. Based on observations from the mechanical stratigraphy, geometric relationships in map and cross-section, as well as morphological considerations, we argue that the origin of the MFF in the area of the considered section is related to active roof duplexes rather than basement-involved thrusting.
Facies analysis and sequence stratigraphy of the uppermost Jurassic– Lower Cretaceous Sulaiy Formation in outcrops of central Saudi Arabia
Authors: Wolpert Philipp , Bartenbach Martin , Suess Peter , Rausch Randolf , Aigner Thomas , Le Nindre Yves-Michel 
Published: October 2021

ABSTRACT
Uppermost Jurassic–Lower Cretaceous carbonates of the Sulaiy Formation are well exposed at the type locality Dahal Hit, and along the entire natural escarpment near Ar Riyad, the capital of the Kingdom of Saudi Arabia. This study provides a facies and sequence-stratigraphic analysis based on detailed sedimentological and gamma-ray logging of 12 outcrop sections. The sections represent the Sulaiy Formation along a 60 km-long outcrop belt, including the Hith-Sulaiy transition in a large solution cavity named Dahal Hit, situated south of Ar Riyad. The latter section is studied in detail because it is the only locality in Saudi Arabia where the Hith Anhyrite (Hith Formation in this study) to the Sulaiy Formation transition crops out.
Ten lithofacies types were identified for the Sulaiy Formation including potential reservoirs such as oolitic cross-bedded grainstones, biostromal boundstones, and bioclast-rich, graded pack-to-grainstones. Lithofacies types are grouped into five facies associations: (1) offshoal, (2) transition zone, foreshoal, (4) shoal margin, and (5) shoal, distributed along a carbonate ramp. Their vertical stacking pattern revealed a systematic hierarchy of cyclicity consisting of small-scale cycles, medium-scale cycle sets and two large-scale sequences for the Sulaiy Formation. Four cycle motifs, with an average thickness of 2–4 m, are present: (1) offshoal to transition zone cycle motif, (2) offshoal to foreshoal cycle motif, (3) transition zone to shoal margin cycle motif, and foreshoal to shoal margin cycle motif.
A total of 15 cycle sets, ranging between 8 and 12 m in thickness each, were interpreted. They were correlated, where possible, across the study area. Three types of medium-scale cycle sets are observed: (1) offshoal to shoal cycle set motif, (2) offshoal to foreshoal cycle set motif, and (3) shoal margin to offshoal cycle set motif. The Lower Sulaiy Sequence consists of twelve cycle sets and is interpreted to contain two Arabian Plate maximum flooding surfaces (MFS): (1) Upper Tithonian MFS J110 (147 Ma) in its lowermost part, which is interpreted to be the time-equivalent of the Manifa reservoir in subsurface Arabia. (2) Lower Berriasian MFS K10 (144 Ma) in the seventh-up cycle set. The Upper Sulaiy Sequence is only represented in the Wadi Nisah Section and is believed to be incomplete because the Sulaiy/Yamama Formation boundary was not included in our study. It is presumed to contain Upper Berriasian MFS K20 (141 Ma).
Facies Composition and Stratigraphic Position of the Quaternary Upper Yenisei Sequence in the Tuva and Minusa Depressions
Authors: Zol’nikov I.D. , Novikov I.S. , Deev E.V. , Shpansky A.V. , Mikharevich M.V. 
Published: October 2021

Abstract
—The paper concerns the sediment sequence, which is widespread in the Yenisei valley and in the Tuva and Minusa depressions and also present in the valleys of the southern Chulym plain. The sediments of this sequence were previously described as “Neogene mud-shedding”, as well as moraines, alluvial fan deposits, alluvium of Middle Pleistocene high terraces, and lacustrine sediments. The giant ripple marks on the Upper Yenisei terraces was commonly interpreted as ribbed moraines; however, in recent studies, these ridges have been repeatedly referred to as marks of giant current ripples. Besides, some recently published papers provide description of geology of this sequence fragments suggesting its deposition by cataclysmic floods. Geomorphological analysis of the area shows Pleistocene glaciers to have been localized within the medium–high mountainous areas. The glaciers did not reach the Tuva and Minusa depressions and occupied large areas only in the Todzha basin and on the periphery of the Darkhat basin, forming a glacial dam at its outlet, which resulted in glacial-dammed lakes filling the basin completely. These lakes outburst, and the resultant flooding led to the deposition of megaflood sediments, which we refer to here as the Upper Yenisei sediment sequence. A detailed analysis of its facies architecture revealed similarity of these sediments to those of the Sal’dzhar and Inya sequences in Gorny Altai. Most of the Upper Yenisei megaflood sediments are localized in topographic lows of the Tuva and Minusa depressions. Beyond the Altai–Sayan mountainous area, the megaflood sediments of the Upper Yenisei sequence compose high terraces of the Yenisei, Chulym, Chet’, and Kiya rivers in the southern Chulym plain. The formation of Upper Yenisei sequence dates to the first half of the Late Pleistocene, inasmuch as it contains inset alluvial sediments of the second terrace of the Yenisei River. The available data allow suggesting that the Upper Yenisei sequence formed in the first Late Pleistocene regional glaciation. The Sal’dzhar sequence in Gorny Altai and the fourth terrace of the Ob’ River on the Fore-Altai plain are stratigraphic analogs of the Upper Yenisei sequence. The Upper Yenisei and Sal’dzhar sequences can thus be considered future regional markers serving as a link for the local stratigraphic schemes of the Altai–Sayan mountainous area and adjacent West Siberian plains. The results obtained call for verification by geochronological dating, first of all, by modern luminescence dating methods covering a wider chronological interval than radiocarbon dating.
Volatile Components in Cordierite and Coexisting Tourmaline and Quartz from Pegmatites of the Kuhilal Deposit (Pamir, Tajikistan)
Authors: Zatolokina K.I. , Tomilenko A.A. , Bul’bak T.A. , Lepezin G.G. 
Published: October 2021

Abstract
—The compositions of volatile components in cordierite, tourmaline, and quartz from pegmatites of the Kuhilal deposit were studied by pyrolysis-free gas chromatography–mass spectrometry (GC–MS), IR and Raman spectroscopy, and microthermometry, and their comparative analysis was performed. Capillary GC–MS was applied to determine the component composition and relative contents (rel.%) of volatiles from different zones of crystals and fractions of cordierite. It has been established that water and carbon dioxide prevail among them. Among hydrocarbons, aliphatic, cyclic, and oxygenated ones are predominant. Heterocyclic, nitrogenated, and sulfonated compounds have also been found. In tourmaline and quartz, volatile components are present in gas–liquid inclusions; in cordierites, they are localized both in structural cavities and in nonstructural positions.
Fetal Hematopoiesis is Driven by Privileged Expansion and Differentiation of HSC-Independent Erythro-Myeloid Progenitors
Authors: Freyer Laina , Iturri Lorea , Biton Anne , Sommer Alina , Dardenne Pascal , Cumano Ana , Perdiguero Elisa Gomez 
Published: October 2021

Abstract
Most blood and immune cells are produced by Hematopoietic Stem Cells (HSC) throughout life. However, several tissue resident immune populations can only be generated from developmentally restricted progenitors. This questions to what extent fetal HSC differentiate in utero, implicating an essential role for HSC-independent progenitors in supporting embryonic viability and innate immunity in the perinatal period. Among them, Erythro-Myeloid Progenitors (EMP) emerge from the extraembryonic yolk sac prior to HSC and their progeny (resident macrophages and skin mast cells) persist in adulthood. Here, we showed that HSC contributed minimally to fetal myelopoiesis as we exposed a developmentally-restricted privilege for erythro-myeloid differentiation from EMP in the fetal liver. EMP-derived myeloid progenitors displayed distinct molecular features and were functionally inequivalent to fetal HSC-derived counterparts. These findings inform future studies of HSC-dependent and HSC-independent hematopoiesis in view of neonatal immunity and pediatric blood disorders for which the cell of origin is poorly understood.
The study of the intention to leave work and its relationship with job burnout among midwives: the long-lasting impacts of COVID-19
Authors: ahmadi sahar , maleki azam 
Published: October 2021

Abstract
Background: It is important to evaluate the long-term effects of the Covid 19 epidemic on the tendency of midwives to leave their jobs. The study was aimed to examine the intention to leave work and its relationship with job burnout among midwives working at Ayatollah Mousavi hospital of Zanjan one year after the Covid-19 disease. In a descriptive-analytical study, the tendency of 88 midwives to leave their jobs was evaluated one year after the outbreak of Covid disease in 2021. The midwives were selected by convenience sampling methods. Data were collected using the Maslach burnout questionnaire and Attwood and Hinshaw tendency to leave the job. Data analyzed by descriptive statistics, Chi-square test, Pearson correlation coefficient, multiple linear regression model with the stepwise method at 95% confidence level.Results:The mean tendency to leave the job was 29.71 ± 6.75. Most of the midwives have a moderate level of the tendency to leave the job (47.7%). There was a significant positive correlation between all three components of burnout and the tendency to leave the job. The odds of leaving the job were 0.344 times higher in people with high emotional fatigue and 0.276 times in people with rotational shift work.Conclusion:It can be concluded that the tendency to leave the job was moderate. Given the relationship between emotional fatigue and the tendency to leave the job, planning to increase the mental strength and resilience of midwives during the epidemic of COVID-19 seems necessary.
Spatiotemporal, Kinematic and Kinetic Assessment of the Effects of a Foot Drop Stimulator for Home-Based Rehabilitation of Patients with Chronic Stroke -- A Three-Dimensional Motion Analysis
Authors: Mao Yurong , Zhao Jiangli , Bian Minjie , Lo Wai Leung Ambrose , Leng Yan , Bian Ruihao , Huang Dongfeng 
Published: October 2021

Abstract
Background: Gait disability affects the daily lives of patients with stroke in both home and community settings. An abnormal foot–ankle position can cause instability on the supporting surface and negatively affect gait. Our research team explored the ability of a portable peroneal nerve-targeting electrical stimulator to improve gait ability by adjusting the foot–ankle position during walking in patients with chronic stroke undergoing home-based rehabilitation. Methods: This was a double-blinded, parallel-group randomized controlled trial. Thirty-one patients with chronic stroke and ankle–foot motor impairment were randomized to receive 3 weeks of gait training, which involved using the transcutaneous peroneal nerve stimulator while walking (tPNS group; n = 16, mean age: 52.25 years), or conventional home and/or community gait training therapy (CT group; n = 15, mean age: 54.8 years). Functional assessments were performed before and after the 3-week intervention. The outcome measures included spatiotemporal gait parameters, three-dimensional kinematic and kinetic data on the ankle-foot joint, and a clinical motor and balance function assessment based on the Fugl–Meyer Assessment of Lower Extremity (FMA-LE) and Berg Balance scales (BBS). Additionally, 16 age-matched healthy adults served as a baseline control of three-dimensional gait data for both trial groups.Results: The FMA-LE and BBS scores improved in both the tPNS groups (p = .004 and .001, respectively) and CT groups (p = .034 and .028, respectively) from before to after training. Participants in the tPNS group exhibited significant differences in spatiotemporal gait parameters, including opposite foot off, double support, stride length, and walking speed, after training (p = .010, .042, .017 and .001, respectively). Additionally, the tPNS group exhibited significant differences in kinematic parameters, such as the ankle angle at the transverse plane (p = .021) and foot progression angle at the frontal plane (p = .009) upon initial contact, and the peak ankle joint angle at the transverse plane (p = .023) and foot progression angle at the frontal and transverse planes (p = .032 and .046, respectively) during gait cycles after 3 weeks of training.Conclusions: Use of a portable tPNS device during walking tasks appeared to improve spatiotemporal gait parameters and ankle and foot angles more effectively than conventional home rehabilitation in patients with chronic stroke. Although guidelines for home-based rehabilitation training services and an increasing variety of market devices are available, no evidence for improvement of motor function and balance was superior to conventional rehabilitation.Trial registration: Chictr, ChiCTR2000040137. Registered 22 November 2020, https://www.chictr.org.cn/showproj.aspx?proj=64424
A Comparative Analysis of Single Cell Small RNA Sequencing Data Reveals Heterogenous Isomir Expression and Regulation.
Authors: Smith Christopher Michael , Hutvagner Gyorgy 
Published: October 2021

Abstract
MicroRNAs (miRNAs) are non-coding small RNAs which play a critical role in the regulation of gene expression in cells. It is known that miRNAs are often expressed as multiple isoforms, called isomiRs, which may have alternative regulatory functions. Despite the recent development of several single cell small RNA sequencing protocols, these methods have not been leveraged to investigate isomiR expression and regulation to better understand their role on a single cell level. Here we integrate sequencing data from three independent studies and find substantial differences in isomiR composition that suggest that cell autonomous mechanisms may drive isomiR processing. We also find evidence of altered regulatory functions of different classes of isomiRs, when compared to their respective wild-type miRNA, which supports a biological role for many of the isomiRs that are expressed.
DeepMicrobeFinder Sorts Metagenomes into Prokaryotes, Eukaryotes and Viruses, with Marine Applications
Authors: Hou Shengwei , Cheng Siliangyu , Chen Ting , Fuhrman Jed A. , Sun Fengzhu 
Published: October 2021

Abstract
Sequence classification is valuable for reducing the complexity of metagenomes and providing a fundamental understanding of the composition of metagenomic samples. Binary metagenomic classifiers offer an insufficient solution because metagenomes of most natural environments are typically derived from multiple sequence sources including prokaryotes, eukaryotes and the viruses of both. Here we introduce a deep-learning based (not reference-based) sequence classifier, DeepMicrobeFinder, that classifies metagenomic contigs into five sequence classes, e.g., viruses infecting prokaryotic or eukaryotic hosts, eukaryotic or prokaryotic chromosomes, and prokaryotic plasmids. At different sequence lengths, DeepMicrobeFinder achieved area under the receiver operating characteristic curve (AUC) scores >0.9 for most sequence classes, the exception being distinguishing prokaryotic chromosomes from plasmids. By benchmarking on 20 test datasets with variable sequence class composition, we showed that DeepMicrobeFinder obtained average accuracy scores of ~0.94, ~0.87, and ~0.92 for eukaryotic, plasmid and viral contig classification respectively, which were significantly higher than the other state-of-the-art individual predictors. Using a 1-300 µm daily time-series metagenomic dataset sampled from coastal Southern California as a case study, we showed that metagenomic read proportions recruited by eukaryotic contigs could be doubled with DeepMicrobeFinder’s classification compared to the counterparts of other reference-based classifiers. In addition, a positive correlation could be observed between eukaryotic read proportions and potential prokaryotic community growth rates, suggesting an enrichment of fast-growing copiotrophs with increased eukaryotic particles. With its inclusive modeling and unprecedented performance, we expect DeepMicrobeFinder will promote metagenomic studies of under-appreciated sequence types.
Effect of Commercial Slow-Release Urea Product on in Vitro Rumen Fermentation and Ruminal Microbial Community Using RUSITEC Technique
Authors: Guo Yongmei , Xiao Ling , Jin Long , Yan Sumei , Niu Dongyan , Yang Wenzhu 
Published: October 2021

Abstract
Background

The objectives of this study were to determine the effect of commercial slow-release urea (SRU) on in vitro fermentation characteristics, nutrient digestibility, gas production, microbial protein synthesis and bacterial community using rumen simulation technique (RUSITEC). The experiment was a completely randomized design with four treatments and four replications of each treatment. Treatments were: control diet (no SRU addition), control diet plus 0.28% SRU (U28), or plus 0.56% SRU (U56), and control diet that was modified for substituting with 0.35% SRU for equavelant soybean protein (MU35; dry matter [DM] basis). The experiment consisted of 8 days of adaptation and 7 days of data and sample collection. Rumen inoculum was obtained from three ruminally fistulated Angus cows fed the same diet to the substrate incubated.
Results

Digestibility of DM, organic matter (OM), crude protein (CP), fibre and starch was not affected, but daily production of gas (P < 0.07) and methane (P < 0.05) was quadratically changed with increasing SRU supplementation. The increase of SRU addition did not affect fermentation pH and total volatile fatty acid (VFA) production, whereas linearly (P < 0.01) decreased proportion of propionate, and linearly (P < 0.01) increased acetate to propionate ratio and ammonia nitrogen (N) concentration. The microbial N efficiency also linearly (P < 0.03) improved with increasing supplementation of SRU. In comparison with control diet, the dietary substitution of SRU for part of soybean meal increased (P < 0.05) the digestibility of DM, OM and CP and decreased (P < 0.02) the total gas production. The total VFA production and acetate to propionate ratio did not differ between control and MU35, whereas the proportion of butyrate was lower (P < 0.05) and that of branched-chain VFA was greater (P < 0.05) with MU35 than control diet. Total and liquid-associated microbial N production as well as ammonia N concentration were greater (P < 0.03) with MU35 than control diet. Observed OTUs, Shannon diversity index, and beta diversity of the microbial community did not differ among treatments. Taxonomic analysis revealed no effect of adding SRU on the relative abundance of bacteria at the phylum level, while at the genus level, the impact of SRU addition on microbial community was greater with MU35 either for liquid associate bacteria or feed particle-associated bacteria.
Conclusions

Supplementation of a dairy cow diet with SRU showed potential of increase in ammonia N concentration and microbial protein production, and change fermentation pattern to more acetate production. Adding SRU in dairy cow diet also showed beneficial effect on improving digestibility of OM and fibre. The results suggest that SRU can partially substitute soybean meal in dairy cow diet to increase microbial protein production without impairing rumen fermentation.
Conditional power, predictive power and probability of success in clinical trials with continuous, binary and time-to-event endpoints
Authors: Kundu Madan Gopal , Samanta Sandipan , Mondal Shoubhik 
Published: October 2021

Abstract
Assessment of study success using conditional power (CP), the predictive power of success (PPoS) and probability of success (PoS) is becoming increasingly common for resource optimization and adaption of trials in clinical investigation. Determination of these measures is often a non-trivial mathematical task. Further, the terminologies used across the literature are not consistent, and there is no consolidated presentation on this. Lastly, certain types of trials received more attention where others (e.g., single-arm trial with time-to-event endpoints) were completely ignored. We attempted to fill these gaps. This paper first provides a detailed derivation of CP, PPoS and PoS in a general setting with normally distributed test statistics and normal prior. Subsequently, expressions for these measures are obtained for continuous, binary, and time-to-event endpoints in single-arm and two-arm trial settings. We have discussed both clinical success and trial success. Importantly, we have derived the expressions for CP, PPoS and PoS in a single-arm trial with a time-to-event endpoint that was never addressed in the literature to our knowledge. In that discussion, we have also shown that commonly recommended 1/d consistently under-estimates the variance of log(median) and alternative expression for variance was derived. We have also presented the PPoS calculation for the binomial endpoint with a beta prior. Examples are given along with the comparison of CP and PPoS. Expressions presented in this paper are implemented in LongCART package in R. An R shiny app is also available at https://ppos.herokuapp.com/ .