bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations between floods and bacillary dysentery cases in main urban areas of Chongqing, China, 2005–2016: a retrospective study
Authors: Ma Yang , Wen Tong , Xing Dianguo , Zhang Yan 
Published: April 2021

Abstract
Background
Understanding the association between floods and bacillary dysentery (BD) incidence is necessary for us to assess the health risk of extreme weather events. This study aims at exploring the association between floods and daily bacillary dysentery cases in main urban areas of Chongqing between 2005 and 2016 as well as evaluating the attributable risk from floods.

Methods
The association between floods and daily bacillary dysentery cases was evaluated by using distributed lag non-linear model, controlling for meteorological factors, long-term trend, seasonality, and day of week. The fraction and number of bacillary dysentery cases attributable to floods was calculated. Subgroup analyses were conducted to explore the association across age, gender, and occupation.

Results
After controlling the impact of temperature, precipitation, relative humidity, long-term trend, and seasonality, a significant lag effect of floods on bacillary dysentery cases was found at 0-day, 3-day, and 4-day lag, and the cumulative relative risk (CRR) over a 7-lag day period was 1.393 (95%CI 1.216–1.596). Male had higher risk than female. People under 5 years old and people aged 15–64 years old had significantly higher risk. Students, workers, and children had significantly higher risk. During the study period, based on 7-lag days, the attributable fraction of bacillary dysentery cases due to floods was 1.10% and the attributable number was 497 persons.

Conclusions
This study confirms that floods can increase the risk of bacillary dysentery incidence in main urban areas of Chongqing within an accurate time scale, the risk of bacillary dysentery caused by floods is still serious. The key population includes male, people under 5 years old, students, workers, and children. Considering the lag effect of floods on bacillary dysentery, the government and public health emergency departments should advance to the emergency health response in order to minimize the potential risk of floods on public.
Modeling transcriptional regulation using gene regulatory networks based on multi-omics data sources
Authors: Patel Neel , Bush William S. 
Published: April 2021

Abstract
Background
Transcriptional regulation is complex, requiring multiple cis (local) and trans acting mechanisms working in concert to drive gene expression, with disruption of these processes linked to multiple diseases. Previous computational attempts to understand the influence of regulatory mechanisms on gene expression have used prediction models containing input features derived from cis regulatory factors. However, local chromatin looping and trans-acting mechanisms are known to also influence transcriptional regulation, and their inclusion may improve model accuracy and interpretation. In this study, we create a general model of transcription factor influence on gene expression by incorporating both cis and trans gene regulatory features.

Results
We describe a computational framework to model gene expression for GM12878 and K562 cell lines. This framework weights the impact of transcription factor-based regulatory data using multi-omics gene regulatory networks to account for both cis and trans acting mechanisms, and measures of the local chromatin context. These prediction models perform significantly better compared to models containing cis-regulatory features alone. Models that additionally integrate long distance chromatin interactions (or chromatin looping) between distal transcription factor binding regions and gene promoters also show improved accuracy. As a demonstration of their utility, effect estimates from these models were used to weight cis-regulatory rare variants for sequence kernel association test analyses of gene expression.

Conclusions
Our models generate refined effect estimates for the influence of individual transcription factors on gene expression, allowing characterization of their roles across the genome. This work also provides a framework for integrating multiple data types into a single model of transcriptional regulation.
Molecular characterization of cytidine monophospho-N-acetylneuraminic acid hydroxylase (CMAH) gene and frequency of blood types in stray cats of İzmir, Turkey
Authors: Can Hüseyin , Erkunt Alak Sedef , Köseoğlu Ahmet Efe , Şahar Umut , Bostanbaş Berna , Baydarlı Serdar , Döşkaya Mert , Ün Cemal 
Published: April 2021

AbstractBackgroundCytidine monophospho-n-acetylneuraminic acid hydroxylase(CMAH) gene associated with blood groups in cats encodes CMAH enzyme that converts Neu5Ac to Neu5Gc. Although variations inCMAHgene of pedigree cats have been revealed, the presence/lack of them in non-pedigree stray cats is unknown. Therefore, the present study aimed to investigate the variations inCMAHgene and the quantity of Neu5Ac and Neu5Gc on erythrocytes of non-pedigree stray cats (n:12) living in İzmir, Turkey. Also, the frequency of blood types was determined in 76 stray cats including 12 cats that were used forCMAHand Neu5A/Neu5Gc analysis.ResultsIn total, 14 SNPs were detected in 5’UTR as well as in exon 2, 4, 9, 10, 11 and 12 ofCMAHgene. Among these SNPs, -495 C > T in 5’UTR was detected for the first time as heterozygous in type A and AB cats, and homozygous and heterozygous in type B cats. The remaining 13 that have been detected in previous studies were also found as homozygous or heterozygous. Both Neu5Gc and Neu5Ac were detected in type A and AB cats. In type B cats, only Neu5Ac was detected. Among two type AB cats, the level of Neu5Ac was found higher in cat carrying heterozygous form (T/C) of 1392T > C. The prevalence of type B cats (67.1 %) was higher than others.ConclusionsThe presence of a new SNP as well as previous SNPs indicates that more variations can be found in stray cats with a more comprehensive study in the future. Also, the high prevalence of type B cats demonstrates the possible risk of neonatal isoerythrolysis among stray cats living in İzmir, Turkey.
Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa
Authors: Wu Qi , Luo Yiming , Wu Xiaoyong , Bai Xue , Ye Xueling , Liu Changying , Wan Yan , Xiang Dabing , Li Qiang , Zou Liang , Zhao Gang 
Published: April 2021

Abstract
Background
Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal.

Results
In this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes.

Conclusions
Together, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.
Bacterial community in saline farmland soil on the Tibetan plateau: responding to salinization while resisting extreme environments
Authors: Li Yi Qiang , Chai Ying Hui , Wang Xu Sheng , Huang Li Ying , Luo Xi Ming , Qiu Cheng , Liu Qing Hai , Guan Xiang Yu 
Published: April 2021

Abstract
Background
Salinization damages the health of soil systems and reduces crop yields. Responses of microbial communities to salinized soils and their functional maintenance under high salt stress are valuable scientific problems. Meanwhile, the microbial community of the salinized soil in the plateau environment is less understood. Here, we applied metagenomics technology to reveal the structure and function of microorganisms in salinized soil of the Tibetan Plateau.

Results
The diversity of composition and function of microbial community in saline soil have changed significantly. The abundances of chemoautotrophic and acidophilic bacteria comprising Rhodanobacter, Acidobacterium, Candidatus Nitrosotalea, and Candidatus Koribacter were significantly higher in saline soil. The potential degradation of organic carbon in the saline soil, as well as the production of NO and N2O via denitrification, and the production of sulfate by sulfur oxidation were significantly higher than the non-saline soil. Both types of soils were rich in genes encoding resistance to environmental stresses (i.e., cold, ultraviolet light, and hypoxia in Tibetan Plateau). The resistance of the soil microbial communities to the saline environment is based on the absorption of K+ as the main mechanism, with cross-protection proteins and absorption buffer molecules as auxiliary mechanisms in our study area. Network analysis showed that functional group comprising chemoautotrophic and acidophilic bacteria had significant positive correlations with electrical conductivity and total sulfur, and significant negative correlations with the total organic carbon, pH, and available nitrogen. The soil moisture, pH, and electrical conductivity are likely to affect the bacterial carbon, nitrogen, and sulfur cycles.

Conclusions
These results indicate that the specific environment of the Tibetan Plateau and salinization jointly shape the structure and function of the soil bacterial community, and that the bacterial communities respond to complex and harsh living conditions. In addition, environmental feedback probably exacerbates greenhouse gas emissions and accelerates the reduction in the soil pH. This study will provide insights into the microbial responses to soil salinization and the potential ecological risks in the special plateau environment.
Adaptation of cucumber seedlings to low temperature stress by reducing nitrate to ammonium during it’s transportation
Authors: Liu Yumei , Bai Longqiang , Sun Mintao , Wang Jun , Li Shuzhen , Miao Li , Yan Yan , He Chaoxing , Yu Xianchang , Li Yansu 
Published: April 2021

Abstract
Background
Low temperature severely depresses the uptake, translocation from the root to the shoot, and metabolism of nitrate and ammonium in thermophilic plants such as cucumber (Cucumis sativus). Plant growth is inhibited accordingly. However, the availability of information on the effects of low temperature on nitrogen transport remains limited.

Results
Using non-invasive micro-test technology, the net nitrate (NO3−) and ammonium (NH4+) fluxes in the root hair zone and vascular bundles of the primary root, stem, petiole, midrib, lateral vein, and shoot tip of cucumber seedlings under normal temperature (NT; 26 °C) and low temperature (LT; 8 °C) treatment were analyzed. Under LT treatment, the net NO3− flux rate in the root hair zone and vascular bundles of cucumber seedlings decreased, whereas the net NH4+ flux rate in vascular bundles of the midrib, lateral vein, and shoot tip increased. Accordingly, the relative expression of CsNRT1.4a in the petiole and midrib was down-regulated, whereas the expression of CsAMT1.2a–1.2c in the midrib was up-regulated. The results of 15N isotope tracing showed that NO3−-N and NH4+-N uptake of the seedlings under LT treatment decreased significantly compared with that under NT treatment, and the concentration and proportion of both NO3−-N and NH4+-N distributed in the shoot decreased. Under LT treatment, the actual nitrate reductase activity (NRAact) in the root did not change significantly, whereas NRAact in the stem and petiole increased by 113.2 and 96.2%, respectively.

Conclusions
The higher net NH4+ flux rate in leaves and young tissues may reflect the higher NRAact in the stem and petiole, which may result in a higher proportion of NO3− being reduced to NH4+ during the upward transportation of NO3−. The results contribute to an improved understanding of the mechanism of changes in nitrate transportation in plants in response to low-temperature stress.
Identification of consistent QTL for time to maturation in Virginia-type Peanut (Arachis hypogaea L.)
Authors: Kunta Srinivas , Agmon Sara , Chedvat Ilan , Levy Yael , Chu Ye , Ozias-Akins Peggy , Hovav Ran 
Published: April 2021

AbstractBackgroundTime-to-maturation (TTM) is an important trait contributing to adaptability, yield and quality in peanut (Arachis hypogaeaL). Virginia market-type peanut belongs to the late-maturingA. hypogaeasubspecies with considerable variation in TTM within this market type. Consequently, planting and harvesting schedule of peanut cultivars, including Virginia market-type, need to be optimized to maximize yield and grade. Little is known regarding the genetic control of TTM in peanut due to the challenge of phenotyping and limited DNA polymorphism. Here, we investigated the genetic control of TTM within the Virginia market-type peanut using a SNP-based high-density genetic map. A recombinant inbred line (RIL) population, derived from a cross between two Virginia-type cultivars ‘Hanoch’ and ‘Harari’ with contrasting TTM (12–15 days on multi-years observations), was phenotyped in the field for 2 years following a randomized complete block design. TTM was estimated by maturity index (MI). Other agronomic traits like harvest index (HI), branching habit (BH) and shelling percentage (SP) were recorded as well.ResultsMI was highly segregated in the population, with 13.3–70.9% and 28.4–80.2% in years 2018 and 2019. The constructed genetic map included 1833 SNP markers distributed on 24 linkage groups, covering a total map distance of 1773.5 cM corresponding to 20 chromosomes on the tetraploid peanut genome with 1.6 cM mean distance between the adjacent markers. Thirty QTL were identified for all measured traits. Among the four QTL regions for MI, two consistent QTL regions (qMIA04a,bandqMIB03a,b) were identified on chromosomes A04 (118680323–125,599,371; 6.9Mbp) and B03 (2839591–4,674,238; 1.8Mbp), with LOD values of 5.33–6.45 and 5–5.35 which explained phenotypic variation of 9.9–11.9% and 9.3–9.9%, respectively. QTL for HI were found to share the same loci as MI on chromosomes B03,B05, and B06, demonstrating the possible pleiotropic effect of HI on TTM. Significant but smaller effects on MI were detected for BH, pod yield and SP.ConclusionsThis study identified consistent QTL regions conditioning TTM for Virginia market-type peanut. The information and materials generated here can be used to further develop molecular markers to select peanut idiotypes suitable for diverse growth environments.
Character changes and Transcriptomic analysis of a cassava sexual Tetraploid
Authors: Chen Xia , Lai Hanggui , Li Ruimei , Yao Yuan , Liu Jiao , Yuan Shuai , Fu Shaoping , Hu Xinwen , Guo Jianchun 
Published: April 2021

Abstract
Background
Cassava (Manihot esculenta Crantz) is an important food crop known for its high starch content. Polyploid breeding is effective in its genetic improvement, and use of 2n gametes in sexual polyploid breeding is one of the potential methods for cassava breeding and improvement. In our study, the cassava sexual tetraploid (ST), which carries numerous valuable traits, was successfully generated by hybridizing 2n female gametes SC5 (♀) and 2n male gametes SC10 (♂). However, the molecular mechanisms remain unclear. To understand these underlying molecular mechanisms behind the phenotypic alterations and heterosis in ST plants, we investigated the differences in gene expression between polyploids and diploids by determining the transcriptomes of the ST plant and its parents during the tuber root enlargement period. We also compared the characters and transcriptomes of the ST plant with its parents.

Results
The ST plant was superior in plant height, stem diameter, leaf area, petiole length, plant weight, and root weight than the parent plants, except the leaf number, which was lower. The number of starch granules was higher in the roots of ST plants than those in the parent plants after five months (tuber root enlargement period), which could be due to a higher leaf net photosynthetic rate leading to early filling of starch granules. Based on transcriptome analysis, we identified 2934 and 3171 differentially expressed genes (DEGs) in the ST plant as compared to its female and male parents, respectively. Pathway enrichment analyses revealed that flavonoid biosynthesis and glycolysis/gluconeogenesis were significantly enriched in the ST plants, which might contribute to the colors of petiole (purple-red), root epidermis (dark brown), and tuber starch accumulation, respectively.

Conclusions
After sexual polyploidization, the phenotype of ST has changed significantly in comparison to their diploid parents, mainly manifest as enlarged biomass, yield, early starch filling, deep colored petiole and root epidermis. The tetraploid plants were also mature early due to early starch grain filling. Owing to enriched flavonoid biosynthesis and glycolysis/gluconeogenesis, they are possibly resistant to adversity stresses and provide better yield, respectively.
The effect of preoperative aminophylline on the recovery profile after major pelvic-abdominal surgeries: a randomized controlled double-blinded study
Authors: Kasim Samaa A. , Bahr Mahmoud Hussein , Abdelkader Mohamed , Rashwan Doaa Abu Elkassim 
Published: April 2021

Abstract
Background
This study compared the effects of premedication with different doses of aminophylline on the recovery profile after general anaesthesia.

Methods
Forty-five patients scheduled for pelvic-abdominal surgeries were divided into 3 groups: Group C: the patients received 100 ml of IV normal saline, Group A1: the patients received 2 mg/kg IV aminophylline, and Group A2: the patients received 4 mg/kg IV aminophylline 30 min before induction of general anaesthesia. The following data were recorded: demographic data, ASA physical status, duration of anaesthesia and surgery, heart rate, mean arterial blood pressure, propofol dose, fentanyl dose, times to reach BIS (48 ± 2) after induction of anaesthesia and to reach a value of 80 after discontinuation of sevoflurane anaesthesia, time to recovery of consciousness and to tracheal extubation and to discharge from the post-anaesthesia care unit, and side effects of aminophylline.

Results
The time to reach a BIS of 48 ± 2 was significantly lower for the control group than group A2 (70.67 ± 22.50 and 106.67 ± 34.77 s for groups C and A2, respectively, p -value =0.01). The time to reach a BIS of 80 was significantly longer for the control group than group A1 andA2 (5.6 ± 1.40,3.5 ± 1.93and 2.53 ± 1.72 min for groups C,A1 and A2, respectively, p -value < 0.01). The time to ROC was significantly longer for the control group than groups A1 and A2 (8.93 ± 0.92, 5.6 ± 2.47 and 4.53 ± 3.33 min for groups C, A1 and A2, respectively; p -value < 0.01). The extubation time was significantly longer for the control group than groups A1 and A2 (12.4 ± 1.08, 7.87 ± 3.27 and 6.6 ± 2.47 min for groups C, A1 and A2, respectively; p -value < 0.01).

Conclusion
Premedication with aminophylline enhanced the recovery profile after pelvic-abdominal surgeries under general anaesthesia without cardiovascular complications.

Clinical trial registration
Name of the registry: Register@ClinicalTrials.gov
Trial registration number: ClinicalTrials.gov Identifier: NCT04151381.
Date of registration, November 5, 2019, ‘Retrospectively registered’.
Intention-to-treat analysis may be more conservative than per protocol analysis in antibiotic non-inferiority trials: a systematic review
Authors:   for the McMaster Infectious Diseases Fellow Research Group, Bai Anthony D. , Komorowski Adam S. , Lo Carson K. L. , Tandon Pranav , Li Xena X. , Mokashi Vaibhav , Cvetkovic Anna , Findlater Aidan , Liang Laurel , Tomlinson George , Loeb Mark , Mertz Dominik 
Published: April 2021

AbstractBackgroundIn non-inferiority trials, there is a concern that intention-to-treat (ITT) analysis, by including participants who did not receive the planned interventions, may bias towards making the treatment and control arms look similar and lead to mistaken claims of non-inferiority. In contrast, per protocol (PP) analysis is viewed as less likely to make this mistake and therefore preferable in non-inferiority trials. In a systematic review of antibiotic non-inferiority trials, we compared ITT and PP analyses to determine which analysis was more conservative.MethodsIn a secondary analysis of a systematic review, we included non-inferiority trials that compared different antibiotic regimens, used absolute risk reduction (ARR) as the main outcome and reported both ITT and PP analyses. All estimates and confidence intervals (CIs) were oriented so that a negative ARR favored the control arm, and a positive ARR favored the treatment arm. We compared ITT to PP analyses results. The more conservative analysis between ITT and PP analyses was defined as the one having a more negative lower CI limit.ResultsThe analysis included 164 comparisons from 154 studies. In terms of the ARR, ITT analysis yielded the more conservative point estimate and lower CI limit in 83 (50.6%) and 92 (56.1%) comparisons respectively. The lower CI limits in ITT analysis favored the control arm more than in PP analysis (median of − 7.5% vs. -6.9%,p = 0.0402). CIs were slightly wider in ITT analyses than in PP analyses (median of 13.3% vs. 12.4%,p < 0.0001). The median success rate was 89% (interquartile range IQR 82 to 93%) in the PP population and 44% (IQR 23 to 60%) in the patients who were included in the ITT population but excluded from the PP population (p < 0.0001).ConclusionsContrary to common belief, ITT analysis was more conservative than PP analysis in the majority of antibiotic non-inferiority trials. The lower treatment success rate in the ITT analysis led to a larger variance and wider CI, resulting in a more conservative lower CI limit. ITT analysis should be mandatory and considered as either the primary or co-primary analysis for non-inferiority trials.Trial registrationPROSPERO registration numberCRD42020165040.