bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prolonged survival of venereal
Tritrichomonas foetus
parasite in the gastrointestinal tract, bovine fecal extract, and water
Authors: Martínez Cristian I. , Iriarte Lucrecia S. , Salas Nehuen , Alonso Andrés M. , Pruzzo Cesar I. , dos Santos Melo Tuanne , Pereira-Neves Antonio , de Miguel Natalia , Coceres Veronica M. 
Published: October 2023

ABSTRACT

Bovine tritrichomonosis is a venereal disease that causes economic losses around the world. Over the last 100 years, the life cycle of the protozoan
Tritrichomonas foetus
in bovines has only considered venereal transmission, almost exclusively through natural mating from an infected animal to a healthy animal. Here, we provide the first direct evidence that
T. foetus
can survive the passage through the gastrointestinal tract in bovines. We demonstrated that the parasite can be discharged by feces in orally infected animals and contaminate the cow’s reproductive tract. We showed that the parasite is capable of surviving at pH conditions usually found along the bovine gastrointestinal tract, and our findings suggest that the parasites could survive in bovine feces and water for several days, probably through the formation of resistant pseudocysts or cyst-like structures. Taken together, our results demonstrate that
T. foetus
is more resistant to adverse external conditions than previously considered, which could be relevant for the life cycle of this parasite in bovines.

IMPORTANCE

Nowadays, the routine herd diagnosis is usually performed exclusively on bulls, as they remain permanently infected, and prevention and control of
Tritrichomonas foetus
transmission are based on identifying infected animals and culling practices. The existence of other forms of transmission and the possible role of pseudocysts or cyst-like structures as resistant forms requires rethinking the current management and control of this parasitic disease in the future in some livestock regions of the world.
G-quadruplexes of KSHV oriLyt play important roles in promoting lytic DNA replication
Authors: Dabral Prerna , Uppal Timsy , Verma Subhash C. 
Published: October 2023

ABSTRACT
Kaposi’s sarcoma-associated herpesvirus (KSHV) utilizes distinct origins of DNA replication (origin of replications) during the latent and lytic phases of its life cycle. Lytic DNA replication requires the participation of cellular and viral proteins to initiate replication at a specific region in the KSHV genome, oriLyt. These regions contain multiple secondary structures and binding sites for viral and cellular proteins. We discovered the presence of G-quadruplex (G4) sites in the oriLyt region. G-quadruplexes are secondary structures in nucleic acid sequences that are considered regulators of multiple biological processes, such as transcription, translation, and replication initiation. Importantly, herpesviruses have a high density of putative quadruplex sequence or formation sites in their genome, including in the regulatory regions, which control replication and transcription. The binding of RecQ1 to the oriLyt region of KSHV and its ability to unwind the G4 structures led us to speculate that G-quadruplex sites play an important role in lytic DNA replication. In this study, we confirmed the formation of stable G-quadruplexes through biochemical and biophysical assays. We further demonstrated that RecQ1, a helicase, associates with the G-quadruplex forming sites of the oriLyt. The functional significance of G4 sites and RecQ1 was confirmed through the stabilization of G4 and depletion of RecQ1 levels through shRNA. Furthermore, the detection of replication initiation through single-molecule analysis of the replicated DNA demonstrated that G4 stabilization leads to subdued replication initiation at the oriLyt. This confirmed the role of the G-quadruplex in regulating viral DNA replication, which can be used to control virus growth.

IMPORTANCE
Biological processes originating from the DNA and RNA can be regulated by the secondary structures present in the stretch of nucleic acids, and the G-quadruplexes are shown to regulate transcription, translation, and replication. In this study, we identified the presence of multiple G-quadruplex sites in the region (oriLyt) of Kaposi’s sarcoma-associated herpesvirus (KSHV) DNA, which is essential for DNA replication during the lytic cycle. We demonstrated the roles of these G-quadruplexes through multiple biochemical and biophysical assays in controlling replication and efficient virus production. We demonstrated that KSHV achieves this by recruiting RecQ1 (helicase) at those G-quadruplex sites for efficient viral DNA replication. Analysis of the replicated DNA through nucleoside labeling and immunostaining showed a reduced initiation of DNA replication in cells with a pharmacologic stabilizer of G-quadruplexes. Overall, this study confirmed the role of the G-quadruplex in regulating viral DNA replication, which can be exploited for controlling viral DNA replication.
Ecosystem heating experiment reveals sex-specific growth responses in fish
Authors: van Dorst Renee M. , Gårdmark Anna , Kahilainen Kimmo K. , Nurminen Leena , Estlander Satu , Huuskonen Hannu , Olin Mikko , Rask Martti , Huss Magnus 
Published: October 2023

Size-specific body growth responses to warming are common among animal taxa, but sex-specific responses are poorly known. Here we ask if body growth responses to warming are sex-dependent, and if such sex-specific responses vary with size and age. This was tested with sex-specific data of back-calculated individual growth trajectories, in European perch ( Perca fluviatilis) from a long-term whole-ecosystem warming experiment (6.3 °C above the surrounding sea). Warming led to both size- and sex-specific differences in growth responses. Warming had a consistent positive effect on body growth of females, but negative effects on male growth at size > 10 cm and age > 2 years. These sex-specific growth responses translate to an increased degree of female-biased sexual size dimorphism (in length-at-age) with warming. Although the exact temperature-mediated effects underlying differential growth responses could not be resolved, results imply global warming may have highly different effects during ontogeny of male and female perch. Such effects should be considered in climate warming scenarios concerning fish growth, population size-structure, and dynamics of aquatic food webs that include fish exhibiting sexual size dimorphism.
Investigating the contribution of author- and publication-specific features to scholars’ h-index prediction
Authors: Momeni Fakhri , Mayr Philipp , Dietze Stefan 
Published: October 2023

AbstractEvaluation of researchers’ output is vital for hiring committees and funding bodies, and it is usually measured via their scientific productivity, citations, or a combined metric such as the h-index. Assessing young researchers is more critical because it takes a while to get citations and increment of h-index. Hence, predicting the h-index can help to discover the researchers’ scientific impact. In addition, identifying the influential factors to predict the scientific impact is helpful for researchers and their organizations seeking solutions to improve it. This study investigates the effect of the author, paper/venue-specific features on the future h-index. For this purpose, we used a machine learning approach to predict the h-index and feature analysis techniques to advance the understanding of feature impact. Utilizing the bibliometric data in Scopus, we defined and extracted two main groups of features. The first relates to prior scientific impact, and we name it ‘prior impact-based features’ and includes the number of publications, received citations, and h-index. The second group is ‘non-prior impact-based features’ and contains the features related to author, co-authorship, paper, and venue characteristics. We explored their importance in predicting researchers’ h-index in three career phases. Also, we examined the temporal dimension of predicting performance for different feature categories to find out which features are more reliable for long- and short-term prediction. We referred to the gender of the authors to examine the role of this author’s characteristics in the prediction task. Our findings showed that gender has a very slight effect in predicting the h-index. Although the results demonstrate better performance for the models containing prior impact-based features for all researchers’ groups in the near future, we found that non-prior impact-based features are more robust predictors for younger scholars in the long term. Also, prior impact-based features lose their power to predict more than other features in the long term.
Information reconciliation of continuous-variables quantum key distribution: principles, implementations and applications
Authors: Yang Shenshen , Yan Zhilei , Yang Hongzhao , Lu Qing , Lu Zhenguo , Cheng Liuyong , Miao Xiangyang , Li Yongmin 
Published: October 2023

AbstractQuantum key distribution (QKD) can provide information-theoretically secure keys for two parties of legitimate communication, and information reconciliation, as an indispensable component of QKD systems, can correct errors present in raw keys based on error-correcting codes. In this paper, we first describe the basic knowledge of information reconciliation and its impact on continuous variable QKD. Then we introduce the information schemes and the corresponding error correction codes employed. Next, we introduce the rate-compatible codes, the hardware acceleration of the reconciliation algorithm, the research progress of information reconciliation, and its application in continuous variable QKD. Finally, we discuss the future challenges and conclude.
Parrondo-Like Behavior in Continuous-Time Random Walks with Periodically Alternating Jumps
Authors: Lee Jiyeon 
Published: October 2023

As a natural generalization of the discrete-time random walk, the continuous-time random walk (CTRW) has been applied to stochastic models with random dynamics in various fields. In this paper, we show that the deterministic alternation of two unbiased CTRWs can lead to a phenomenon similar to the Parrondo paradox, in which the asymptotic mean drift of the combined CTRW becomes positive or negative depending on the parameter values. This extends the case in which the paradox occurs due to the random combination of two CTRWs with memory shown by Montero [Phys. Rev. E 84 (2011) 051139].
Stochastic dynamics and data science
Authors: Gao Ting , Duan Jinqiao 
Published: October 2023

Recent advances in data science are opening up new research fields and broadening the range of applications of stochastic dynamical systems. Considering the complexities in real-world systems (e.g., noisy data sets and high dimensionality) and challenges in mathematical foundation of machine learning, this review presents two perspectives in the interaction between stochastic dynamical systems and data science. On the one hand, deep learning helps to improve first principle-based methods for stochastic dynamical systems. AI for science, combining machine learning methods with available scientific understanding, is becoming a valuable approach to study stochastic dynamical systems with the help of observation data. On the other hand, a challenge is the theoretical explanations for deep learning. It is crucial to build explainable deep learning structures with the help of stochastic dynamical systems theory in order to demonstrate how and why deep learning works. In this review, we seek better understanding of the mathematical foundation of the state-of-the-art techniques in data science, with the help of stochastic dynamical systems, and we further apply machine learning tools for studying stochastic dynamical systems. This is achieved through stochastic analysis, algorithm development, and computational implementation. Topics involved with this review include Stochastic Analysis, Dynamical Systems, Inverse Problems, Data Assimilation, Numerical Analysis, Optimization, Nonparametric Statistics, Uncertainty Quantification, Deep Learning, and Deep Reinforcement Learning. Moreover, we emphasize available analytical tools for non-Gaussian fluctuations in scientific and engineering modeling.
Multimodal Dialog Systems with Dual Knowledge-enhanced Generative Pretrained Language Model
Authors: Chen Xiaolin , Song Xuemeng , Jing Liqiang , Li Shuo , Hu Linmei , Nie Liqiang 
Published: October 2023

Text response generation for multimodal task-oriented dialog systems, which aims to generate the proper text response given the multimodal context, is an essential yet challenging task. Although existing efforts have achieved compelling success, they still suffer from two pivotal limitations: (1)
overlook the benefit of generative pretraining
and (2)
ignore the textual context-related knowledge
. To address these limitations, we propose a novel dual knowledge-enhanced generative pretrained language mode for multimodal task-oriented dialog systems (DKMD), consisting of three key components:
dual knowledge selection
,
dual knowledge-enhanced context learning
, and
knowledge-enhanced response generation
. To be specific, the dual knowledge selection component aims to select the related knowledge according to both textual and visual modalities of the given context. Thereafter, the dual knowledge-enhanced context learning component targets seamlessly, integrating the selected knowledge into the multimodal context learning from both global and local perspectives, where the cross-modal semantic relation is also explored. Moreover, the knowledge-enhanced response generation component comprises a revised BART decoder, where an additional dot-product knowledge-decoder attention sub-layer is introduced for explicitly utilizing the knowledge to advance the text response generation. Extensive experiments on a public dataset verify the superiority of the proposed DKMD over state-of-the-art competitors.
Toward a Better Understanding of Randomized Greedy Matching
Authors: Tang Zhihao Gavin , Wu Xiaowei , Zhang Yuhao 
Published: October 2023

There has been a long history of studying randomized greedy matching algorithms since the work by Dyer and Frieze [9]. We follow this trend and consider the problem formulated in the oblivious setting, in which the vertex set of a graph is known to the algorithm but not the edge set. The algorithm can make queries for the existence of the edge between any pair of vertices but must include the edge into the matching if it exists, i.e., as in the query-commit model by Gamlath et al. [12]. We revisit theModified Randomized Greedy (MRG)algorithm by Aronson et al. [1] that is proved to achieve a (0.5+ε)-approximation. In each step of the algorithm, an unmatched vertex is chosen uniformly at random and matched to a randomly chosen neighbor (if exists). We study a weaker version of the algorithm namedRandom Decision Order (RDO)that, in each step, randomly picks an unmatched vertex and matches it to an arbitrary neighbor (if exists). We prove that theRDOalgorithm provides a 0.639-approximation for bipartite graphs and 0.531-approximation for general graphs. As a corollary, we substantially improve the approximation ratio ofMRG.Furthermore, we generalize theRDOalgorithm to the edge-weighted case and prove that it achieves a 0.501-approximation ratio. This result solves the open question by Chan et al. [4] and Gamlath et al. [12] about the existence of an algorithm that beats greedy in edge-weighted general graphs, where the greedy algorithm probes the edges in descending order of edge-weights. We also present a variant of the algorithm that achieves a (1-1/e)-approximation for edge-weighted bipartite graphs, which generalizes the (1-1/e)-approximation ratio of Gamlath et al. [12] for the stochastic setting to the case when the realizations of edges are arbitrarily correlated, where in the stochastic setting, there is a known probability associated with each pair of vertices that indicates the probability that an edge exists between the two vertices, when the pair is probed.
Surgical versus Interventional Mitral Valve Repair: Analysis of 1,100 Propensity Score-Matched Patients
Authors: Amabile Andrea , Muncan Brandon , Geirsson Arnar , Kalogeropoulos Andreas P. , Krane Markus 
Published: October 2023

Objective. We aimed to investigate outcomes in transcatheter versus surgical mitral valve repair in patients with secondary mitral regurgitation (MR) by leveraging a global, multi-institutional federated network database. Methods. Using validated ICD-10 and CPT codes, the TriNetX Analytics Research Data Network (a global federated database of electronic health records from 58 healthcare organizations) was queried to identify patients diagnosed with chronic, severe, ischemic MR and undergoing either transcatheter mitral valve repair (TMVr) or surgical mitral valve repair (SMVr) between January 1, 2015 and December 31, 2020. To adjust for baseline differences, 1 : 1 propensity score matching was performed via logistic regression using the nearest-neighbor approach and matching for 29 covariates including demographics, comorbidities, surgical history, preoperative medications, left ventricular function and heart failure status. We compared 1- and 3-year mortality rates and 1- and 3-year mitral valve reoperation rates in the matched cohorts using Kaplan-Meier estimates and adjusted Cox proportional hazards models. Results. A total of 2,352 patients met inclusion criteria (1,392 in the surgical mitral valve repair group and 960 in the TMVr group). After 1 : 1 propensity score matching, a total of 550 patients undergoing surgical mitral valve repair (SMVr) were compared to 550 patients undergoing TMVr. All characteristics were adequately matched between the cohorts (standardized mean difference <0.1). At 1- and 3-years respectively, mortality rate was 13.4% and 20.7% for surgical patients and 19.8% and 40.3% for TMVr patients. When compared to TMVr, patients undergoing SMVr were significantly less likely to face mortality at 3 years (HR: 0.42, 95% CI: 0.31–0.56,

p

<

0.0001

). At 1- and 3-years respectively, mitral valve reoperation was 2.2%, and 2.4% for surgical patients and 6.6% and 7.8% for TMVr patients. When compared to TMVr, patients undergoing SMVr were significantly less likely to undergo mitral valve reintervention at 3 years (HR: 0.29, 95% CI: 0.14–0.58, p = 0.0002). Conclusion. In a real-world, propensity score matching analysis of a large cohort of patients with chronic ischemic MR, surgical mitral valve repair had significantly better survival rates and significantly lower reintervention rates at 1- and 3-years compared to TMVr.
A Pilot Study of Paricalcitol plus Nanoliposomal Irinotecan and 5-FU/LV in Advanced Pancreatic Cancer Patients after Progression on Gemcitabine-Based Therapy
Authors: Grierson Patrick M. , Suresh Rama , Tan Benjamin , Pedersen Katrina S. , Amin Manik , Park Haeseong , Trikalinos Nikolaos A. , Liu Jingxia , Boice Nicholas , Brown Amberly , Bansod Sapana , Wang-Gillam Andrea , Lim Kian-Huat 
Published: October 2023

Abstract

Purpose:
Vitamin D analogues remodel the desmoplastic stroma, and improve vascularity and efficacy of chemotherapy in preclinical pancreas cancer models.

Patients and Methods:
We conducted a pilot study to evaluate the safety and preliminary efficacy of the vitamin D analogue paricalcitol in combination with nanoliposomal irinotecan (Nal-iri) plus 5-fluorouracil/leucovorin (5-FU/LV) in patients with advanced pancreatic cancer who had progressed on gemcitabine-based therapy. Two dose levels (DL) of paricalcitol were tested: fixed dose weekly (75 mcg, DL1) and weight-based weekly (7 mcg/kg, /DL2). The primary endpoint was safety, and secondary endpoints included overall response rate, progression-free survival (PFS), and overall survival (OS). Correlative objectives aimed to identify molecular predictors of response and alterations in the tumor stroma.

Results:
Twenty patients (10 each in DL1 and DL2) enrolled between March 2019 and May 2021. No grade 3/4 adverse events related to paricalcitol were observed. The most common toxicities were nausea, diarrhea and fatigue, which were similar in both cohorts. Three patients discontinued study after one cycle and were not radiographically evaluable. Of the remaining 17 evaluable patients, 2 had partial response and 12 had stable disease. The median PFS for response-evaluable patients in DL1 was 4.14 months, for DL2 was 4.83 months. Intent-to-treat median OS was 6.15 and 6.66 months for DL1 and DL2, respectively. Correlative studies showed increased tumor vascularity in posttreatment samples in patients receiving the higher dose of paricalcitol (DL2).

Conclusions:
Paricalcitol at 7 mcg/kg/week in combination with Nal-iri/ 5-FU/LV is safely tolerated, may increase tumor vascularity and warrants further investigation.
Sleep Variability, Sleep Irregularity, and Nighttime Blood Pressure Dipping
Authors: Xu Yanyan , Barnes Vernon A. , Harris Ryan A. , Altvater Michelle , Williams Celestine , Norland Kimberly , Looney Jacob , Crandall Reva , Su Shaoyong , Wang Xiaoling 
Published: October 2023

BACKGROUND:
Circadian rhythm regulates many important biological functions in humans. The goal of this study is to explore the impact of day-to-day deviations in the sleep-wake cycle on nighttime blood pressure (BP) dipping and further examine whether the ethnic difference in day-to-day deviations in sleep patterns can explain the ethnic difference in nighttime BP dipping.

METHODS:
Twenty-four-hour ambulatory BP monitoring and 7-day accelerometer data were obtained from 365 adult participants (age range, 18.7–50.1 years; 52.6% Black participants and 47.3% European Americans; 64.1% females). Systolic BP dipping level was used to represent nighttime BP dipping. The SD of sleep duration was calculated as the index of sleep variability, and the SD of sleep midpoint was calculated as the index of sleep irregularity.

RESULTS:

A 1-hour increase in the SD of sleep midpoint was associated with a 1.16% decrease in nighttime BP dipping (
P
<0.001). A 1-hour increase in the SD of sleep duration was associated with a 1.39% decrease in nighttime BP dipping (
P
=0.017). The ethnic difference in the SD of sleep midpoint can explain 29.2% of the ethnicity difference in BP dipping (
P
=0.008).

CONCLUSIONS:
Sleep variability and sleep irregularity are associated with blunted BP dipping in the general population. In addition, data from the present investigation also demonstrate that the ethnic difference in sleep irregularity could partly explain the ethnic difference in BP dipping, an important finding that may help reduce the health disparity between Black participants and European Americans.