bluuebunny/crossref_metadata_2025_split huggingface dataset:
EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning
Authors: Zhou Bailing , Ding Maolin , Feng Jing , Ji Baohua , Huang Pingping , Zhang Junye , Yu Xue , Cao Zanxia , Yang Yuedong , Zhou Yaoqi , Wang Jihua 
Published: December 2022

Abstract
Long non-coding RNAs (lncRNAs) played essential roles in nearly every biological process and disease. Many algorithms were developed to distinguish lncRNAs from mRNAs in transcriptomic data and facilitated discoveries of more than 600 000 of lncRNAs. However, only a tiny fraction (&lt;1%) of lncRNA transcripts (~4000) were further validated by low-throughput experiments (EVlncRNAs). Given the cost and labor-intensive nature of experimental validations, it is necessary to develop computational tools to prioritize those potentially functional lncRNAs because many lncRNAs from high-throughput sequencing (HTlncRNAs) could be resulted from transcriptional noises. Here, we employed deep learning algorithms to separate EVlncRNAs from HTlncRNAs and mRNAs. For overcoming the challenge of small datasets, we employed a three-layer deep-learning neural network (DNN) with a K-mer feature as the input and a small convolutional neural network (CNN) with one-hot encoding as the input. Three separate models were trained for human (h), mouse (m) and plant (p), respectively. The final concatenated models (EVlncRNA-Dpred (h), EVlncRNA-Dpred (m) and EVlncRNA-Dpred (p)) provided substantial improvement over a previous model based on support-vector-machines (EVlncRNA-pred). For example, EVlncRNA-Dpred (h) achieved 0.896 for the area under receiver-operating characteristic curve, compared with 0.582 given by sequence-based EVlncRNA-pred model. The models developed here should be useful for screening lncRNA transcripts for experimental validations. EVlncRNA-Dpred is available as a web server at https://www.sdklab-biophysics-dzu.net/EVlncRNA-Dpred/index.html, and the data and source code can be freely available along with the web server.
Auditory cortical connectivity in humans
Authors: Rolls Edmund T , Rauschecker Josef P , Deco Gustavo , Huang Chu-Chung , Feng Jianfeng 
Published: December 2022

AbstractTo understand auditory cortical processing, the effective connectivity between 15 auditory cortical regions and 360 cortical regions was measured in 171 Human Connectome Project participants, and complemented with functional connectivity and diffusion tractography. 1. A hierarchy of auditory cortical processing was identified from Core regions (including A1) to Belt regions LBelt, MBelt, and 52; then to PBelt; and then to HCP A4. 2. A4 has connectivity to anterior temporal lobe TA2, and to HCP A5, which connects to dorsal-bank superior temporal sulcus (STS) regions STGa, STSda, and STSdp. These STS regions also receive visual inputs about moving faces and objects, which are combined with auditory information to help implement multimodal object identification, such as who is speaking, and what is being said. Consistent with this being a “what” ventral auditory stream, these STS regions then have effective connectivity to TPOJ1, STV, PSL, TGv, TGd, and PGi, which are language-related semantic regions connecting to Broca’s area, especially BA45. 3. A4 and A5 also have effective connectivity to MT and MST, which connect to superior parietal regions forming a dorsal auditory “where” stream involved in actions in space. Connections of PBelt, A4, and A5 with BA44 may form a language-related dorsal stream.
Dynamic causal modeling of cerebello-cerebral connectivity when sequencing trait-implying actions
Authors: Pu Min , Ma Qianying , Haihambo Naem , Li Meijia , Baeken Chris , Baetens Kris , Deroost Natacha , Heleven Elien , Van Overwalle Frank 
Published: December 2022

Abstract
Prior studies suggest that the cerebellum contributes to the prediction of action sequences as well as the detection of social violations. In this dynamic causal modeling study, we explored the effective connectivity of the cerebellum with the cerebrum in processing social action sequences. A first model aimed to explore functional cerebello-cerebral connectivity when learning trait/stereotype-implying action sequences. We found many significant bidirectional connectivities between mentalizing areas of the cerebellum and the cerebrum including the temporo-parietal junction (TPJ) and medial prefrontal cortex (mPFC). Within the cerebrum, we found significant connectivity between the right TPJ and the mPFC, and between the TPJ bilaterally. A second model aimed to investigate cerebello-cerebral connectivity when conflicting information arises. We found many significant closed loops between the cerebellum and cerebral mentalizing (e.g. dorsal mPFC) and executive control areas (e.g. medial and lateral prefrontal cortices). Additional closed loops were found within the cerebral mentalizing and executive networks. The current results confirm prior research on effective connectivity linking the cerebellum with mentalizing areas in the cerebrum for predicting social sequences, and extend it to cerebral executive areas for social violations. Overall, this study emphasizes the critical role of cerebello-cerebral connectivity in understanding social sequences.
Each coin has 2 sides: a positive role of alien Potamopyrgus antipodarum (Grey, 1843) snails in reducing the infection of native lymnaeids with trematodes
Authors: Cichy Anna , Stanicka Anna , Żbikowska Elżbieta 
Published: December 2022

Abstract
The change in the distribution of organisms in freshwater ecosystems due to natural or manmade processes raises the question of the impact of alien species on local communities. Although most studies indicate a negative effect, the positive one is more difficult to discern, especially in multispecies systems, including hosts and parasites. The purpose of the study was to check whether the presence of an alien host, Potamopyrgus antipodarum, reduces the intensity of Echinoparyphium aconiatum metacercariae in a native host, Radix spp. We additionally tested the impact of water temperature and the biomass of the alien host on the dilution effect. We experimentally studied (1) the lifespan of echinostome cercariae in different temperatures, (2) the infectivity of cercariae toward the alien host and native host, and (3) the impact of different biomass of the alien host on the intensity of metacercariae in the native host. We found that cercarial survival and infectivity were temperature dependent. However, cercarial survival decreased with increasing temperature, contrary to cercarial infectivity. Echinostome cercariae entered the renal cavity of both the native host and alien host, and successfully transformed into metacercariae. The number of metacercariae in the native host decreased with the increasing biomass of the alien host. Our results indicate that lymnaeids may benefit from the co-occurrence with P. antipodarum, as the presence of additional hosts of different origins may reduce the prevalence of parasites in native communities. However, the scale of the dilution effect depends not only on the increased spectrum of susceptible hosts but also on the other variables of the environment, including water temperature and host density.
Learning curve for adoption of robot-assisted minimally invasive esophagectomy: a systematic review of oncological, clinical, and efficiency outcomes
Authors: Pickering Oliver J , van Boxel Gijs I , Carter Nick C , Mercer Stuart J , Knight Benjamin C , Pucher Philip H 
Published: December 2022

Summary
Background: Robot-assisted minimally invasive esophagectomy (RAMIE) is gaining increasing popularity as an operative approach. Learning curves to achieve surgical competency in robotic-assisted techniques have shown significant variation in learning curve lengths and outcomes. This study aimed to summarize the current literature on learning curves for RAMIE. Methods: A systematic review was conducted in line with PRISMA guidelines. Electronic databases PubMed, MEDLINE, and Cochrane Library were searched, and articles reporting on learning curves in RAMIE were identified and scrutinized. Studies were eligible if they reported changes in operative outcomes over time, or learning curves, for surgeons newly adopting RAMIE. Results: Fifteen studies reporting on 1767 patients were included. Nine studies reported on surgeons with prior experience of robot-assisted surgery prior to adopting RAMIE, with only four studies outlining a specified RAMIE adoption pathway. Learning curves were most commonly analyzed using cumulative sum control chart (CUSUM) and were typically reported for lymph node yields and operative times, with significant variation in learning curve lengths (18–73 cases and 20–80 cases, respectively). Most studies reported adoption without significant impact on clinical outcomes such as anastomotic leak; significant learning curves were more likely in studies, which did not report a formal learning or adoption pathway. Conclusion: Reported RAMIE adoption phases are variable, with some authors suggesting significant impact to patients. With robust training through formal programmes or proctorship, however, others report RAMIE adoption without impact on clinical outcomes. A formalized adoption curriculum appears critical to prevent adverse effects on operative efficiency and patient care.
Pathological complete response in multimodal treatment of esophageal cancer: a retrospective cohort study
Authors: Hipp Julian , Kuvendjiska Jasmina , Hillebrecht Hans Christian , Timme-Bronsert Sylvia , Fichtner-Feigl Stefan , Hoeppner Jens , Diener Markus K 
Published: December 2022

Summary
To evaluate pathological complete response (pCR, ypT0ypN0) after neoadjuvant treatment compared with non-complete response (non-CR) in patients with esophageal cancer (EC), and 393 patients were retrospectively analyzed. Survival probability was analyzed in patients with: (i) pCR vs non-CR; (ii) complete response of the primary tumor but persisting lymphatic metastases (non-CR-T0N+) and (iii) pCR and tumor-free lymphnodes exhibiting signs of postneoadjuvant regression vs. no signs of regression. (i) Median overall survival (mOS) was favorable in patients with pCR (pCR: mOS not reached vs. non-CR: 41 months, P &lt; 0.001). Multivariate analysis revealed that grade of regression was not an independent predictor for prolonged survival. Instead, the achieved postneoadjuvant TNM-stage (T-stage: Hazard ratio [HR] ypT3-T4 vs. ypT0-T2: 1.837; N-stage: HR ypN1-N3 vs. ypN0: 2.046; Postneoadjuvant M-stage: HR ypM1 vs. ycM0: 2.709), the residual tumor (R)-classification (HR R1 vs. R0: 4.195) and the histologic subtype of EC (HR ESCC vs. EAC: 1.688) were prognostic factors. Patients with non-CR-T0N+ have a devastating prognosis, similar to those with local non-CR and lymphatic metastases (non-CR-T + N+) (non-CR-T0N+: 22.0 months, non-CR-T + N-: mOS not reached, non-CR-T + N+: 23.0 months; P-values: non-CR-T0N+ vs. non-CR-T + N-: 0.016; non-CR-T0N+ vs. non-CR-T + N+: 0.956; non-CR-T + N- vs. non-CR-T + N+: &lt;0.001). Regressive changes in lymphnodes after neoadjuvant treatment did not influence survival-probability in patients with pCR (mOS not reached in each group; EAC-patients: P = 0.0919; ESCC-patients: P = 0.828). Particularly, the achieved postneoadjuvant ypTNM-stage influences the survival probability of patients with EC. Patients with non-CR-T0N+ have a dismal prognosis, and only true pathological complete response with ypT0ypN0 offers superior survival probabilities.
Differential response to isometric handgrip depending on the heart failure condition in patients with functional mitral regurgitation: a case report
Authors: Hamatani Yasuhiro , Ide Yuya , Watanabe Hirotoshi , Akao Masaharu 
Published: December 2022

AbstractBackgroundFunctional mitral regurgitation (MR) changes dynamically depending on the loading conditions and can cause acute heart failure (HF). Isometric handgrip is a simple stress test and can be performed during early phase of acute HF for the evaluation of MR.Case summaryA 70-year-old woman with a prior myocardial infarction four months before, and with history of recurrent HF admission with functional MR, who received optimal HF medications, was hospitalized for acute HF. On the following day of the admission, isometric handgrip stress echocardiography was performed to evaluate functional MR. During the handgrip, MR deteriorated from moderate to severe and the tricuspid regurgitation pressure gradient increased from 45 to 60 mmHg. After HF stabilization 2 weeks after admission, repeat handgrip stress echocardiography showed that the degree of MR did not significantly change being moderate and the tricuspid regurgitation pressure gradient was only mildly elevated from 25 to 30 mmHg. She underwent transcatheter edge-to-edge mitral repair, and thereafter she has not experienced the rehospitalization for acute HF.DiscussionExercise stress test is recommended for the evaluation of functional MR in HF patients; however, exercise tests are difficult to perform during the early phase of acute HF. In this regard, handgrip test is an option to investigate the exacerbating impact of functional MR during early-phase acute HF. This case indicated that response to isometric handgrip can vary depending on HF condition, highlighting the importance of taking into account the timing of the handgrip procedure in patients with functional MR and HF.
Magnetic properties of surface soils in the upper and middle reaches of the Yarlung Zangbo River Basin, southern Tibetan Plateau, and their environmental significance
Authors: Wang Shuyuan , Chen Zixuan , Yang Junhuai , Gao Fuyuan , Tian Weidong , Ma Xingyue , Xia Dunsheng 
Published: December 2022

SUMMARY
The relationship between climate and the magnetic properties of surface soils on the Chinese Loess Plateau (CLP) have been widely used to provide the basis for palaeoclimatic reconstruction, based on the underlying loess/palaeosol sequences. To date, however, there are few investigations of variations in the magnetic properties of surface soils on the Tibetan Plateau (TP), especially on the southern TP. Therefore, it remains unclear whether magnetic properties could be used as proxies for palaeoclimatic reconstruction in the region. In this study, environmental magnetic parameters and bulk sediment grain-size measurements were made on a set of surface samples from the Yarlung Zangbo River Basin (YZRB), on the southern TP, and their environmental significance was evaluated. The results reveal spatial differences in the magnetic properties of the surface soils, likely caused by regional climatic factors. The input of primary magnetic minerals is the driver of the magnetic properties of the samples from the western (Gar-Saga) part of the YZRB, where the magnetic variations are controlled by the influence of wind intensity on the local source material. However, the samples from the eastern region (Gongga-Nyingchi) are significantly affected by the topographic and sedimentary conditions, and there is no relationship between the magnetic properties and climate. The samples from the central part of the study area (Saga-Gongga) show obvious signs of a pedogenic influence on magnetic properties and ultrafine superparamagnetic (SP) and single domain (SD) ferrimagnetic minerals dominate the magnetic susceptibility. Combined with the variation of grain size, this implies the influence of wind intensity and pedogenesis contribute to the magnetic enhancement. However, the pedogenic intensity closely related to precipitation and temperature could offer the possibility of using sedimentary magnetic properties for palaeoclimatic reconstruction. Furthermore, the existence of a distinct pedogenic alteration boundary in the Saga area is consistent with the location of the Indian summer monsoon, which may be the dominant control on the pedogenic intensity.
An empirical investigation into the impact of winner’s curse on estimates from Mendelian randomization
Authors: Jiang Tao , Gill Dipender , Butterworth Adam S , Burgess Stephen 
Published: December 2022

AbstractIntroductionGenetic associations for variants identified through genome-wide association studies (GWASs) tend to be overestimated in the original discovery data set as, if the association was underestimated, the variant may not have been detected. This bias, known as winner’s curse, can affect Mendelian randomization estimates, but its severity and potential impact are unclear.MethodsWe performed an empirical investigation to assess the potential bias from winner’s curse in practice. We considered Mendelian randomization estimates for the effect of body mass index (BMI) on coronary artery disease risk. We randomly divided a UK Biobank data set 100 times into three equally sized subsets. The first subset was treated as the ‘discovery GWAS’. We compared genetic associations estimated in the discovery GWAS to those estimated in the other subsets for each of the 100 iterations.ResultsFor variants associated with BMI at P &lt; 5 × 10–8 in at least one iteration, genetic associations with BMI were up to 5-fold greater in iterations in which the variant was associated with BMI at P &lt; 5 × 10–8 compared with its mean association across all iterations. If the minimum P-value for association with BMI was P = 10–13 or lower, then this inflation was &lt;25%. Mendelian randomization estimates were affected by winner’s curse bias. However, bias did not materially affect results; all analyses indicated a deleterious effect of BMI on coronary artery disease risk.ConclusionsWinner’s curse can bias Mendelian randomization estimates, although its practical impact may not be substantial. If avoiding sample overlap is infeasible, analysts should consider performing a sensitivity analysis based on variants strongly associated with the exposure.
Effects of a Saccharomyces cerevisiae fermentation product on fecal characteristics, metabolite concentrations, and microbiota populations of dogs subjected to exercise challenge
Authors: Oba Patrícia M , Carroll Meredith Q , Sieja Kelly M , de Souza Nogueira Juliana P , Yang Xiaojing , Epp Tammi Y , Warzecha Christine M , Varney Jessica L , Fowler Jason W , Coon Craig N , Swanson Kelly S 
Published: December 2022

Abstract
The objective of this study was to determine the fecal characteristics, microbiota, and metabolites of dogs fed a Saccharomyces cerevisiae fermentation product (SCFP) and subjected to exercise challenge in untrained and trained states. Thirty-six adult dogs (18 male, 18 female; mean age: 7.1 yr; mean body weight: 29.0 kg) were randomly assigned to control or SCFP-supplemented (250 mg/dog/d) diets and fed for 10 wk. After 3 wk, dogs were given an exercise challenge (6.5 km run), with fresh fecal samples collected pre- and post-challenge. Dogs were then trained by a series of distance-defined running exercise regimens over 7 wk (two 6.4 km runs/wk for 2 wk; two 9.7 km runs/wk for 2 wk; two 12.9 km runs/wk for 2 wk; two 3.2 km runs/wk). Dogs were then given exercise challenge (16 km run) in the trained state, with fresh fecal samples collected pre- and post-challenge. Fecal microbiota data were evaluated using QIIME2, while all other data were analyzed using the Mixed Models procedure of SAS. Effects of diet, exercise, and diet*exercise were tested with P &lt; 0.05 considered significant. Exercise challenge reduced fecal pH and ammonia in both treatments, and in untrained and trained dogs. After the exercise challenge in untrained dogs, fecal indole, isobutyrate, and isovalerate were reduced, while acetate and propionate were increased. Following the exercise challenge in trained dogs, fecal scores and butyrate decreased, while isobutyrate and isovalerate increased. SCFP did not affect fecal scores, pH, dry matter, or metabolites, but fecal Clostridium was higher in controls than in SCFP-fed dogs over time. SCFP and exercise challenge had no effect on alpha or beta diversity in untrained dogs. However, the weighted principal coordinate analysis plot revealed clustering of dogs before and after exercise in trained dogs. After exercise challenge, fecal Collinsella, Slackia, Blautia, Ruminococcus, and Catenibacterium were higher and Bacteroides, Parabacteroides, Prevotella, Phascolarctobacterium, Fusobacterium, and Sutterella were lower in both untrained and trained dogs. Using qPCR, SCFP increased fecal Turicibacter, and tended to increase fecal Lactobacillus vs. controls. Exercise challenge increased fecal Turicibacter and Blautia in both untrained and trained dogs. Our findings show that exercise and SCFP may affect the fecal microbiota of dogs. Exercise was the primary cause of the shifts, however, with trained dogs having more profound changes than untrained dogs.
Glycine regulates lipid peroxidation promoting porcine oocyte maturation and early embryonic development
Authors: Gao Lepeng , Zhang Chang , Zheng Yingying , Wu Deyi , Chen Xinyuan , Lan Hainan , Zheng Xin , Wu Hao , Li Suo 
Published: December 2022

Abstract
In vitro-cultured oocytes are separated from the follicular micro-environment in vivo and are more vulnerable than in vivo oocytes to changes in the external environment. This vulnerability disrupts the homeostasis of the intracellular environment, affecting oocyte meiotic completion, and subsequent embryonic developmental competence in vitro. Glycine, one of the main components of glutathione (GSH), plays an important role in the protection of porcine oocytes in vitro. However, the protective mechanism of glycine needs to be further clarified. Our results showed that glycine supplementation promoted cumulus cell expansion and oocyte maturation. Detection of oocyte development ability showed that glycine significantly increased the cleavage rate and blastocyst rate during in vitro fertilization (IVF). SMART-seq revealed that this effect was related to glycine-mediated regulation of cell membrane structure and function. Exogenous addition of glycine significantly increased the levels of the anti-oxidant GSH and the expression of anti-oxidant-related genes (glutathione peroxidase 4 [GPX4], catalase [CAT], superoxide dismutase 1 [SOD1], superoxide dismutase 2 [SOD2], and mitochondrial solute carrier family 25, member 39 [SLC25A39]), decreased the lipid peroxidation caused by reactive oxygen species (ROS) and reduced the level of malondialdehyde (MDA) by enhancing the functions of mitochondria, peroxisomes and lipid droplets (LDs) and the levels of lipid metabolism-related factors (peroxisome proliferator activated receptor coactivator 1 alpha [PGC-1α], peroxisome proliferator-activated receptor γ [PPARγ], sterol regulatory element binding factor 1 [SREBF1], autocrine motility factor receptor [AMFR], and ATP). These effects further reduced ferroptosis and maintained the normal structure and function of the cell membrane. Our results suggest that glycine plays an important role in oocyte maturation and later development by regulating ROS-induced lipid metabolism, thereby protecting against biomembrane damage.
The Evolution of the ‘Trade and …’ ‘Debate’—A View from ASEAN
Authors: Hsu Locknie 
Published: December 2022

ABSTRACT
This article explores the ‘Trade and …’ ‘Debate’ in the context of trade and environment issues. It provides an explanation of the evolution of discussions of such issues in a non-dispute settlement context, using developments in the Association of Southeast Asian Nations’ integration efforts as illustrations. It also highlights a number of opportunities for trade and environment collaboration in negotiations for free trade agreement and Digital Economy Partnership Agreements.