bluuebunny/crossref_metadata_2025_split huggingface dataset:
Function analysis of ZmZHD9, a positive regulator in drought stress response in transgenic maize
Authors: Zhang Pengyu , Wei Li , Cao Liru , Qiu Xiao , Fu Jiaxu , Wang Guorui , Ku Lixia , Wang Tongchao 
Published: December 2020

Abstract
Backgrounds: Drought stress is one of the major factors that affects maize yield. ZF-HD transcription factors have been proved to play pivotal roles in the regulation of plant growth, hormone conduction signaling and abiotic stress response. However, the molecular mechanism of ZmZHD9-mediated drought tolerance is not well understood. Results: In the present study, we analyzed the functions of ZmZHD9, a member of the maize ZF-HD family. ZmZHD9 is predominantly expressed in leaves, and was induced by drought, salinity, high temperature and abscisic acid (ABA). Subcellular localization indicated that ZmZHD9 protein was localized in the nucleus. ZmZHD9-overexpressing plants showed increased tolerance to drought stress compared with wild-type plants, evaluated by higher RWC and proline content, higher SOD and POD activity, lower REL and MDA content in transgenic plants under drought stress. In addition, the expression of six stress-responsive genes were significantly higher in ZmZHD9 transgenic plants than that in wild-type plants under drought stress.Conclusion: These results demonstrate that ZmZHD9 as a stress-responsive transcription factor which plays a positive regulatory role in response to drought.
Optimizing source tracking of Listeria monocytogenes with quasimetagenomics and integrated long and short read sequencing
Authors: Commichaux Seth , Javkar Kiran , Ramachandran Padmini , Nagarajan Niranjan , Bertrand Denis , Chen Yi , Reed Elizabeth , Gonzalez-Escalona Narjol , Strain Errol , Rand Hugh , Pop Mihai , Ottesen Andrea 
Published: December 2020

Abstract
Background: Rapid pathogen detection is essential for an effective public health response. The Illumina MiSeq short read sequencer has been the workhorse of many whole genome sequencing source tracking programs. However, short reads cannot span many bacterial genomic repeats, resulting in highly fragmented assemblies. Long read sequencing can span the repeats resulting in the complete assembly of bacterial genomes. With the advancing throughput and accuracy of inexpensive long read sequencing data, it is important to evaluate this resource for potential inclusion in rapid response pathogen identification protocols.Results: Here we sought to maximize the utility of long read (GridIon, Oxford Nanopore) and short read (MiSeq, Illumina) sequencing data for the identification of Listeria monocytogenes from naturally contaminated ice cream. Aliquots from the temporal enrichment (quasimetagenomes) of L. monocytogenes were sequenced and assembled with 10 different assembly approaches. Long read assembly tools generated genome-length contigs and a circularized 71 kbp putative L. monocytogenes plasmid; however, the high sequencing error rate prevented strain typing at even 150X depth of coverage. Short read assemblies provided accurate core gene strain typing after 28 hours of enrichment but were too fragmented for typing the full gene set and reconstructing a circularized genome and plasmid. Hybrid approaches demonstrated the most promising results but were biased by assembly strategy. Short read assemblies scaffolded with long reads were able to accurately strain type L. monocytogenes after just 24 hours of enrichment, but were still too fragmented for sequence typing the full gene set. Long read assemblies polished with short reads recovered genome-length contigs, the full complement of genes, and a circularized plasmid after 24 hours enrichment; however they could not consistently achieve the core gene strain typing accuracy of short read or short read hybrid assembly approaches. Conclusion: These analyses demonstrate that strategic integration and optimization of microbiological (quasimetagenomic), molecular (integrated long and short reads), and bioinformatic approaches (diverse assembly strategies) can greatly improve our ability to quickly and accurately identify pathogens.
A new Passage Retrieval Method in Arabic Question Answering Systems
Authors: Alsabbagh Lana , AlDakkak Oumayma , Ghneim Nada 
Published: December 2020

Abstract
In this paper, we present our approach to improve the performance of open-domain Arabic Question Answering systems. We focus on the passage retrieval phase which aims to retrieve the most related passages to the correct answer.
To extract passages that are related to the question, the system passes through three phases: Question Analysis, Document Retrieval and Passage Retrieval. We define the passage as the sentence that ends with a dot ".". In the Question Processing phase, we applied the traditional NLP steps of tokenization, stopwords and unrelated symbols removal, and replacing the question words with their stems. We also applied Query Expansion by adding synonyms to the question words. In the Document Retrieval phase, we used the Vector Space Model (VSM) with TF-IDF vectorizer and cosine similarity. For the Passage Retrieval phase, which is the core of our system, we measured the similarity between passages and the question by a combination of the BM25 ranker and Word Embedding approach.
We tested our system on ACRD dataset, which contains 1395 questions in different domains, and the system was able to achieve correct results with a precision of 92.2% and recall of 79.9% in finding the top-3 related passages for the query.
Assessment of COVID-19 knowledge, Preventive behaviors, severity, self-efficacy and mental health in Bangladesh and Iraq
Authors: Hossain Tonazzina , Hashim Hashim Talib , Nasreen Fahtiha , Jwamer Vanya Ibrahim 
Published: December 2020

Abstract
Background: As a part of South- Eastern Asia- Pacific, Bangladesh has been following to adopt proactive non-therapeutic means to repress the spread of nCoV-2 just like other countries. As stated in reports of September, the COVID-19 pandemic has become very distressing in Iraq, a Country in Southwestern Asia Pacific reporting around 4,000 new cases every day and around 500 deaths a week.Methodology: A descriptive, survey-based, cross sectional study was conducted among 1000 participants aged > 18 years old from Bangladesh and Iraq.The survey was conducted as an online survey distributed for the general population for a month. The questions were assessed using Likert-type response scale from 1 to 5 for almost all questions. Chi2, mean and standard deviation were used to present the data. Results: There are significant differences between the mental health assessment, the country, educational level, hypertension and smoking. While the other variables have no effect on mental health. Approximately 99% of the participants said they had heard about COVID-19. More than 90% of the participants have stated that they know about COVID- 19. Also, more than 85% of the participants have claimed that they know the causes of COVID-19. Furthermore, participants (around 84%) were largely aware of the death rate for people infected by the virus. Conclusion: Mental health is mostly affected by the pandemic and need to be regularly assessed to keep the immunity competent. Poverty and lack of proper education are contributing factors in increment of COVID-19 cases and discarding about preventions.
The impact of a COVID-19 pandemic-related interruption of regular physical rehabilitation on functional abilities in a patient with two chronic neurological diseases: a case report
Authors: Braun Tobias , Weidmann Raphael , Möller Jens Carsten , Ammann Anissa , Marks Detlef 
Published: December 2020

Abstract
Background: Regular outpatient rehabilitation is prescribed for many patients with chronic neurological disorders, such as Parkinson's disease or Multiple Sclerosis, to constantly support patients and their proxies in disease management. Due to the COVID-19 pandemic, federal institutions and governments worldwide have directed local or nationwide lockdowns. During these times, the provision of regular outpatient rehabilitation service is drastically limited, making it actually impossible for community-dwelling patients with neurological disorders to receive prescribed rehabilitation interventions.Case presentation: A 67-year-old man with two chronic neurological diseases, Parkinson's disease and Multiple Sclerosis, underwent a 4-week inpatient rehabilitation in our hospital. The patient gained significant functional improvements that he maintained over the following months, supported by the continuation of physiotherapy in the domestic environment. Due to a COVID-19 pandemic related interruption of the regular ambulatory rehabilitation for several weeks, the patient’s functional abilities decreased significantly. Thus, the patient was again referred to our hospital for intensive inpatient rehabilitation to regain his physical functioning and mobility capacity. At hospital discharge, the patient improved most of his physical functioning to a pre-pandemic level.Conclusions: The interruption of a rehabilitation service due to a pandemic-related lockdown can significantly impact the functional abilities of patients with chronic neurological diseases. This case report supports the claim for continuous access to rehabilitation services for all people with rehabilitation needs.
Seropositivity and risk factors of Brucella infection in small ruminants that had history of recent abortion in the afar region of north-eastern Ethiopia
Authors: Tekle Muluken , Legesse Mengistu , Ameni Gobena , Mamo Gezahegne 
Published: December 2020

Abstract
Background: Brucellosis is one of the most important reproductive disease causes abortion and breeding failure in small ruminants and also causes severe systemic diseases in exposed humans. In Ethiopia, several studies of seroprevalence shows the magnitude and distribution of brucellosis both in animals and humans vary in different geographical localities. However, except few studies in Ethiopia all these serological studies was limited to RBPT and CFT, so far not supplemented with a varities of serological tests like ELISA to detect brucella infection, which is increase the likehood of detecting infected individulas and also improve the reliability of epidemiological data for appropriate control strategies. Hence, the present study was conducted in Amibara district of Afar Region, Ethiopia to detect the seropositivity and risk factor of Brucella infection in small ruminants that had history of recent abortion using mRBPT, cELISA and CFT. Materials and methods: Sera were collected from 226 animals (195 goats and 31sheep) and assessed for seropositivity of Brucella infection using modified Rose Bengal Plate Test (mRBPT), Complement Fixation Test (CFT) and competitive Enzyme Linked Immuno Sorbent Assay (cELISA).Results : In this study the over all seroprevalence was 12.0% (27 out of 226), 7.5% (17 out of 226) and 26.6% (60 out of 226) by mRBPT, CFT and cELISA, respectively. Out of 27 sera which were reactive by mRBPT, 17 (63.0%) were also reactive by (CFT). Out of the 17 sera which were reactive by CFT and mRBPT, 14 (82.4%) were reactive by cELISA. Out of the 29 sera which were non-reactive both by mRBPT and CFT, 10 (34.5%) were found to be reactive by cELISA. Out of the 226 sera which were tested both by mRBPT and cELISA, 20 (8.9%) were reactive by both tests, while 159 (70.4%) were non-reactive by both tests. The percentage of test agreement (79.2%) between mRBPT and cELISA was poor (k= 0.353). A high seropositivity for Brucella infection was significantly associated with the presence of retained placenta in the study animals (adjusted OR= 2.2, 95%CI, 1.1-4.4, P=0.030) as detected by cELISA. Conclusion: The findings of this study could suggest that brucellosis is main cause of abortion and breeding failure in small ruminants that had histry of recent abortion in the pastoral communities’ andwarrants the need for proactive measures to reduce its economic impact and risk of zoonotic transmission. This study indicates that cELISA based seroepidemiological survey increase the likehood of detecting infected individulas of brucellosis and also would be useful to provide reliable evidence for Brucella infection in small ruminants compared to mRBPT.
“Side effects--part of the package”: A mixed methods approach to study adverse events among patients being programmatically treated for DR-TB in Gujarat, India
Authors: Jakasania Arjunkumar Hardas , shringarpure Kalpita , Kapadia Dixit , Sharma Radhika , Mehta Kedar , Prajapati Arpit , Soundappan Kathirvel 
Published: December 2020

Abstract
BackgroundHigh rates of Adverse Events (AEs) during treatment is one of the leading causes of unsuccessful treatment outcomes among patients with drug resistant tuberculosis (DR-TB). However, information related to AEs is not systematically collected and managed under programmatic setting. The present study assessed the a) incidence and pattern of adverse events in first three months of DR-TB treatment initiation; b) treatment seeking behaviour for AE management; and c) explore the challenges in seeking treatment and reporting AEs.MethodsThis mixed methods study included all patients diagnosed and initiated on treatment under RNTCP during July-September 2018 at Ahmedabad DR-TB centre. The patients were interviewed telephonically and assessed for all AEs experienced by them. In-depth interviews and key-informant interviews were conducted among patients, DOTS supervisors and programme staffs (treatment supervisors, medical officer and district program manager). Results: Total 207 AEs were reported by the 74 DR-TB patients. All patients experienced at least one AE during initial treatment period. Incidence rate of AEs (experienced) was 3.11 (1st month-4.6, 2nd month-2.7, 3rd month-2.02) per 100 person days. Of the 207 AEs, gastro-intestinal (59, 28.3%), ophthalmic (32, 15.4%) and otolaryngology (25, 11.9%) system related AEs were commonly experienced. Treatment was not sought in two-fifths of the AEs. Themes and sub-themes related to challenges in treatment seeking or reporting of AEs were 1) Patient related-Misconceptions, accessibility and affordability of management, lack of counselling support, stigma and discrimination, and past treatment experience; 2) Health system related- lack of guidelines and training for AE management, 3) Poor coordination between hospital and tuberculosis centre. Conclusion: The incidence of AEs was high among patients with DR-TB in the first three months of treatment and treatment seeking/reporting was low. Adequate health education and counselling of the patient and orientation of the health systems are the need of the hour. An efficient real-time reporting and management of AE should be developed and tested for effective DR-TB control.
The effects of seaward distance on above and below ground carbon stocks in estuarine mangrove ecosystems
Authors: Cleyndert Georgia de Jong , Cuni-Sanchez Aida , Seki Hamidu A , Shirima Deo D , Munishi Pantaleo K.T. , Burgess Neil , Calders Kim , Marchant Robert 
Published: December 2020

Abstract
Background: Mangrove forests have gained recognition for their potential role in climate change mitigation due to carbon sequestration in live trees, and carbon storage in the sediments trapped by mangrove tree roots and pneumatophores. Africa hosts about 19% of the world’s mangroves, yet relatively few studies have examined the carbon stocks of African mangroves. The available studies report considerable differences among sites and amongst the different pools of carbon stocks. None considered the effects of seaward distance. We present details of AGC and SOC carbon stocks for Lindi in Tanzania, and focus on how these values differ with increasing seaward distance and, how our results compare to those reported elsewhere across Africa.Results: AGC ranged between 11-55Mg C ha-1, but was not significantly affected by seaward distance. SOC for 0-1m depth ranged from 154-484, with a mean of 302 Mg C ha-1. SOC was significantly negatively correlated with seaward distance. Mangrove type (estuarine/oceanic), soil erosion, soil depth may explain these differences We note important methodological differences in previous studies on carbon stocks in mangroves in Africa. Conclusion:This study indicates that seaward distance has an important effect on SOC stocks in the Lindi region of Tanzania. SOC should be fully incorporated into national climate change mitigation policies. Studies should report seaward distance and to describe the type of mangrove stand to make results easily comparable across sites and to assess the true value of Blue Carbon in Africa. We recommend focusing on trees >10cm diameter for AGC, and sampling soils to at least 1m depth for SOC, which would provide a more complete assessment of the potentially considerable mangrove carbon store.
The Comparison of Efficacy and Complications of Coblation and Radiofrequency Thermocoagulation for V2/V3 Idiopathic Trigeminal Neuralgia: A Retrospective Cohort Study of 292 Cases
Authors: Wang ChenHui , Dou Zhi , Yan MengWei , Tang Yuanzhang , Zhao Rui , Han YuJie , Ni Jiaxiang 
Published: December 2020

Abstract
Background: Coblation is a novel technique in respect of treating idiopathic trigeminal neuralgia. We aimed to identify the efficacy and complications between radiofrequency thermocoagulation (RFT) and coblation for V2/V3 idiopathic trigeminal neuralgia (ITN) and investigate the risk factors associated with postoperative facial numbness.Methods: We retrospectively reviewed our cohort of 292 patients who had undergone RFT or coblation for V2/V3 ITN. The characteristics of the baseline were collected before surgery. Pain scores, the degree of facial numbness and other complications were evaluated at discharge and 1month, 3 months, 6 months and 12 months after surgery.Results: Postoperative pain intensity was apparently alleviated in both groups. The initial and 12-months remission rates were 94.0% and 75.3% in coblation group compared with 96.9% and 78.4% in RFT group (P=0.462, P=0.585). The degree of postoperative facial numbness tended to be more severe in RFT group at discharge, 1 month, 6 months and 12 months (P=0.006, P=0.026, P=0.004, P=0.003). Factors significantly associated with more severe facial numbness were procedure of RFT (OR=0.46, 95%CI: 0.28-0.76, P=0.002), history of previous RFT at the affected side (OR=2.33, 95%CI: 1.21-4.48, P=0.011), and ITN with concomitant continuous pain (OR=0.36, 95%CI: 0.18-0.71, P=0.004).Conclusion: Coblation could reduce the degree of postoperative facial numbness for ITN, and the efficacy was no less effective than RFT. History of previous RFT at the affected side, procedure of RFT, ITN with concomitant continuous pain was identified as significant factors of the development of postoperative facial numbness.
The cultural practice of removing shoes indoors is relevant to the mortality rate of the SARS-CoV-2 pandemic.
Authors: Iwasaki Soshi , Takahashi Kazunobu , Yamakage Michiaki 
Published: December 2020

Abstract
Japan has had a lower number of SARS-CoV-2 cases than anticipated. Hence, we hypothesize that the habit of removing shoes indoors, which is practiced in various countries, might influence the SARS-CoV-2 transmission patterns and COVID-19 associated morbidity and mortality through transmission-based infection. There are significantly fewer COVID-19 deaths in countries that follow the cultural practice of removing shoes indoors.
Outcome of Community- versus Hospital-Acquired Intra-Abdominal Infections in Intensive Care Unit: a Retrospective Study
Authors: Abaziou Timothée , Vardon-Bounes Fanny , Conil Jean-Marie , Rouget Antoine , Ruiz Stéphanie , Grare Marion , Fourcade Olivier , Suc Bertrand , Leone Marc , Minville Vincent , Georges Bernard 
Published: December 2020

Abstract
Background: To compare patients hospitalised in the intensive care unit (ICU) after surgery for community-acquired intra-abdominal infection (CA-IAI) and hospital-acquired intra-abdominal infection (HA-IAI) in terms of mortality, severity and complications.Methods: Retrospective study including all patients admitted to 2 ICUs within 48 hours of undergoing surgery for peritonitis.Results: 226 patients were enrolled during the study period. Patients with CA-IAI had an increased 28-day mortality rate compared to those with HA-IAI (30% vs 15%, respectively (p = 0.009)). At 90 days, the mortality rates were 36.7% and 37.5% in the CA-IAI group and HA-IAI group, respectively, with a similar APACHE II score on admission (median: 21 [15 – 25] vs. 21 [15 - 24] respectively, p = 0.63). The patients with HA-IAI had prolonged ICU and hospital stays (median: 17 [7 – 36] vs. 6[3 – 12] days, p < 0.001 and 41 [24 – 66] vs. 17 [7 – 32] days, p = 0.001), and experienced more complications (reoperation and reintubation) than those with CA-IAI.Conclusion: CA-IAI group had higher 28-day mortality rate than HA-IAI group. Mortality was similar at 90 days but those with HA-IAI had a prolonged ICU and hospital stay. In addition, they developed more complications.
Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia)
Authors: Feng Shan , Fang Hongcheng , Liu Xia , Dong Yuhui , Wang Qingpeng , Yang Ke Qiang 
Published: December 2020

Abstract
Background: Walnut anthracnose caused by Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. is an important walnut production problem in China. Although the long non-coding RNAs (lncRNAs) are important for plant disease resistance , the molecular mechanisms underlying resistance to C. gloeosporioides in walnut remain poorly understood.Results: The anthracnose-resistant F26 fruits from the B26 clone and the anthracnose-susceptible F423 fruits from the 4-23 clone of walnut were used as the test materials. Specifically, we performed a comparative transcriptome analysis of F26 and F423 fruit bracts to identify differentially expressed LncRNAs (DELs) at five time-points (tissues at 0 hpi, pathological tissues at 24 hpi, 48 hpi, 72 hpi, and distal uninoculated tissues at 120 hpi). Compared with F423, a total of 14525 DELs were identified, including 10645 upregulated lncRNAs and 3846 downregulated lncRNAs in F26. The number of upregulated lncRNAs in F26 compared to in F423 was significantly higher at the early stages of C. gloeosporioides infection. A total of 5 modules related to disease resistance were screened by WGCNA and the target genes of lncRNAs were obtained. Bioinformatic analysis showed that the target genes of upregulated lncRNAs were enriched in immune-related processes during the infection of C. gloeosporioides, such as activation of innate immune response, defense response to bacterium, incompatible interaction and immune system process, and enriched in plant hormone signal transduction, phenylpropanoid biosynthesis and other pathways. And 124 known target genes for 96 hub lncRNAs were predicted, including 10 known resistance genes. The expression of 5 lncRNAs and 5 target genes was confirmed by qPCR, which was consistent with the RNA-seq data.Conclusions: The results of this study provide the basis for future functional characterizations of lncRNAs regarding the C. gloeosporioides resistance of walnut fruit bracts.