bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repetitive DNA profile of the amphibian mitogenome
Authors: Cabañas Noel , Becerra Arturo , Romero David , Govezensky Tzipe , Espinosa-Aguirre Jesús Javier , Camacho-Carranza Rafael 
Published: May 2020

Abstract
Background
Repetitive DNA elements such as direct and inverted repeat sequences are present in every genome, playing numerous biological roles. In amphibians, the functions and effects of the repeat sequences have not been extensively explored. We consider that the data of mitochondrial genomes in the NCBI database are a valuable alternative to generate a better understanding of the molecular dynamic of the repeat sequences in the amphibians.

Results
This work presents the development of a strategy to identify and quantify the total amount of repeat sequences with lengths from 5 to 30 base pairs in the amphibian mitogenomes. The results show differences in the abundance of repeat sequences among amphibians and bias to specific genomic regions that are not easily associated with the classical amphibian ancestry.

Conclusions
Derived from these analyses, we show that great variability of the repeat sequences exists among amphibians, demonstrating that the mitogenomes of these organisms are dynamic.
Antimicrobial sensitivity profile and bacterial isolates among suspected pyogenic meningitis patients attending at Hawassa University Hospital: Cross-sectional study
Authors: Assegu Fenta Demissie , Lemma Kinfe , Tadele Henok , Tadesse Birkneh Tilahun , Derese Birrie 
Published: May 2020

AbstractBackgroundBacterial meningitis is a serious inflammation of the meninges. Antimicrobial therapy on early cerebrospinal fluid (CSF) examination has an important role in diagnosis. The disease is still challenging in developing countries because of poor (diagnostic set-up, socioeconomic conditions, management), and misuse of antimicrobial therapy results in emerging antimicrobial-resistant strains. Therefore, this hospital based cross sectional study was aimed to assess the antimicrobial sensitivity profile and bacterial isolates among patients suspected of pyogenic meningitis at Hawassa University Hospital from February 2017 to 2018.ResultsA total of 394 patients suspected as meningitis were included. Of these 210 (53.3%) were males and 184 (46.7%) were females. The carriage rate of bacterial pathogens was 27(6.9%). The common clinical presentations were fever 330 (83.8%), headache 205 (52.0%) and neck stiffness 179(45.4%) followed by altered mental status 125(31.7%). Neck stiffnessP = 0.001 (AOR = 1.18, 95% CI 1.06–6.53), Hx of seizureP = 0.043, (AOR = 1.39, 95% CI 1.15–5.99), Nuchal rigidityP = 0.001* (AOR = 1.26, 95% CI 1.06–4.48) were significantly associated with culture positivity.The pathogens isolated in this study wereN. meningitidisthe most frequent isolate 12(44.4%) followed byS. pneumoniae5 (18.5%),E. coli4(14.8%),H. influenza3(13.6%),S. aureus2(11.1%) andK. pneumoniae1(3.7%).S. pneumoniaewas (100%) resistance to penicillin, (80%) amoxicillin, and (20%) Cefotaxime.S. aureuswas (100%) resistant to penicillin, amoxicillin, and ciprofloxacin.N. meningitidiswas (100%) resistant to penicillin, (66.7%) Ceftriaxone and (41.7%) chloramphenicol. In this study a single isolate was also resistant to a different antibiotic.ConclusionThe prevention of bacterial meningitis needs serious attention since the isolated bacteria showed single and multiple antimicrobial susceptibility patterns and the variable nature of isolated etiological agents makes it reasonable to provide continuous future updates on local resistance of common antibiotics and optimize the most frequent bacteria associated with meningitis in the hospital. Therefore; further, survey study with a better design of antimicrobial susceptibility at large scale to control the spread of antibiotic-resistant bacteria and the change in the causative organism of bacterial meningitis in the study area and at a national level is required.
Proteome profile changes during poly-hydroxybutyrate intracellular mobilization in gram positive Bacillus cereus tsu1
Authors: Li Hui , O’Hair Joshua , Thapa Santosh , Bhatti Sarabjit , Zhou Suping , Yang Yong , Fish Tara , Thannhauser Theodore W. 
Published: May 2020

Abstract
Background
Bacillus cereus is a bacterial species which grows efficiently on a wide range of carbon sources and accumulates biopolymer poly-hydroxybutyrate (PHB) up to 80% cell dry weight. PHB is an aliphatic polymer produced and stored intracellularly as a reservoir of carbon and energy, its mobilization is a key biological process for sporulation in Bacillus spp. Previously, B. cereus tsu1 was isolated and cultured on rapeseed cake substrate (RCS), with maximum of PHB accumulation reached within 12 h, and depleted after 48 h. Fore-spore and spore structure were observed after 24 h culture.

Results
Quantitative proteomic analysis of B. cereus tsu1 identified 2952 quantifiable proteins, and 244 significantly changed proteins (SCPs) in the 24 h:12 h pair of samples, and 325 SCPs in the 48 h:12 h pair of samples. Based on gene ontology classification analysis, biological processes enriched only in the 24 h:12 h SCPs include purine nucleotide metabolism, protein folding, metal ion homeostasis, response to stress, carboxylic acid catabolism, and cellular amino acid catabolism. The 48 h:12 h SCPs were enriched into processes including carbohydrate metabolism, protein metabolism, oxidative phosphorylation, and formation of translation ternary structure. A key enzyme for PHB metabolism, poly(R)-hydroxyalkanoic acid synthase (PhaC, KGT44865) accumulated significantly higher in 12 h-culture. Sporulation related proteins SigF and SpoEII were significantly higher in 24 h-samples. Enzymes for nitrate respiration and fermentation accumulated to the highest abundance level in 48 h-culture.

Conclusions
Changes in proteome of B. cereus tsu1 during PHB intracellular mobilization were characterized in this study. The key enzyme PhaC for PHB synthesis increased significantly after 12 h-culture which supports the highest PHB accumulation at this time point. The protein abundance level of SpoIIE and SigF also increased, correlating with sporulation in 24 h-culture. Enzymes for nitrate respiration and fermentation were significantly induced in 48 h-culture which indicates the depletion of oxygen at this stage and carbon flow towards fermentative growth. Results from this study provide insights into proteome profile changes during PHB accumulation and reuse, which can be applied to achieve a higher PHB yield and to improve bacterial growth performance and stress resistance.
Genome-wide identification of the expansin gene family reveals that expansin genes are involved in fibre cell growth in cotton
Authors: Lv Li-Min , Zuo Dong-Yun , Wang Xing-Fen , Cheng Hai-Liang , Zhang You-Ping , Wang Qiao-Lian , Song Guo-Li , Ma Zhi-Ying 
Published: May 2020

Abstract
Background
Expansins (EXPs), a group of proteins that loosen plant cell walls and cellulosic materials, are involved in regulating cell growth and diverse developmental processes in plants. However, the biological functions of this gene family in cotton are still unknown.

Results
In this paper, we identified a total of 93 expansin genes in Gossypium hirsutum. These genes were classified into four subfamilies, including 67 GhEXPAs, 8 GhEXPBs, 6 GhEXLAs, and 12 GhEXLBs, and divided into 15 subgroups. The 93 expansin genes are distributed over 24 chromosomes, excluding Ghir_A02 and Ghir_D06. All GhEXP genes contain multiple exons, and each GhEXP protein has multiple conserved motifs. Transcript profiling and qPCR analysis revealed that the expansin genes have distinct expression patterns among different stages of cotton fibre development. Among them, 3 genes (GhEXPA4o, GhEXPA1A, and GhEXPA8h) were highly expressed in the initiation stage, 9 genes (GhEXPA4a, GhEXPA13a, GhEXPA4f, GhEXPA4q, GhEXPA8f, GhEXPA2, GhEXPA8g, GhEXPA8a, and GhEXPA4n) had high expression during the fast elongation stage, and GhEXLA1c and GhEXLA1f were preferentially expressed in the transition stage of fibre development.

Conclusions
Our results provide a solid basis for further elucidation of the biological functions of expansin genes in relation to cotton fibre development and valuable genetic resources for future crop improvement.
Optimization of salicylic acid and chitosan treatment for bitter secoiridoid and xanthone glycosides production in shoot cultures of Swertia paniculata using response surface methodology and artificial neural network
Authors: Kaur Prabhjot , Gupta R. C. , Dey Abhijit , Malik Tabarak , Pandey Devendra Kumar 
Published: May 2020

Abstract
Background
In this study, response surface methodology (RSM) and artificial neural network (ANN) was used to construct the predicted models of linear, quadratic and interactive effects of two independent variables viz. salicylic acid (SA) and chitosan (CS) for the production of amarogentin (I), swertiamarin (II) and mangiferin (III) from shoot cultures of Swertia paniculata Wall. These compounds are the major therapeutic metabolites in the Swertia plant, which have significant role and demand in the pharmaceutical industries.

Results
Present study highlighted that different concentrations of SA and CS elicitors substantially influenced the % yield of (I), (II) and (III) compounds in the shoot culture established on modified ½ MS medium (supplemented with 2.22 mM each of BA and KN and 2.54 mM NAA). In RSM, different response variables with linear, quadratic and 2 way interaction model were computed with five-factor-three level full factorial CCD. In ANN modelling, 13 runs of CCD matrix was divided into 3 subsets, with approximate 8:1:1 ratios to train, validate and test. The optimal enhancement of (I) (0.435%), (II) (4.987%) and (III) (4.357%) production was achieved in 14 days treatment in shoot cultures of S. paniculata elicited by 9 mM and 12 mg L− 1 concentrations (SA) and (CS).

Conclusions
In optimization study, (I) show 0.170–0.435%; (II) display 1.020–4.987% and (III) upto 2.550–4.357% disparity with varied range of SA (1–20 mM) and CS (1–20 mg L− 1). Overall, optimization of elicitors to promote secoiridoid and xanthone glycoside production with ANN modeling (r2 = 100%) offered more significant results as compared to RSM (r2 = 99.8%).

Graphical abstract
Over-expression of a γ-tocopherol methyltransferase gene in vitamin E pathway confers PEG-simulated drought tolerance in alfalfa
Authors: Ma Jiangtao , Qiu Deyun , Gao Hongwen , Wen Hongyu , Wu Yudi , Pang Yongzhen , Wang Xuemin , Qin Yuchang 
Published: May 2020

Abstract
Background
α-Tocopherol is one of the most important vitamin E components present in plant. α-Tocopherol is a potent antioxidant, which can deactivate photoproduced reactive oxygen species (ROS) and prevent lipids from oxidation when plants suffer drought stress. γ-Tocopherol methyltransferase (γ-TMT) catalyzes the formation of α-tocopherol in the tocopherol biosynthetic pathway. Our previous studies showed that over-expression of γ-TMT gene can increase the accumulation of α-tocopherol in alfalfa (Medicago sativa). However, whether these transgenic plants confer increased drought tolerance and the underlying mechanism are still unknown.

Results
In the present study, we further evaluate transgenic alfalfa lines, and found that over-expression of MsTMT led to an increase in α-tocopherol and total tocopherol level in the transgenic lines compared with the control plant. It was revealed that drought tolerance of the transgenic alfalfa was remarkably increased, with alleviated oxidative damage and accumulation of more osmolytic substances. The stomatal development in transgenic plants was significantly inhibited on both sides of leaves, which may be resulted from the repression of MsSPCHLESS (MsSPCH) gene. The reduced stomatal density of transgenic plants contributes to a lower stomatal conductance and higher water use efficiency (WUE). Moreover, both RNA-seq and qRT-PCR analyses indicate that regulatory mechanism of MsTMT in drought involved in both ABA-dependent and ABA-independent pathways.

Conclusion
Our results suggest that MsTMT gene plays a positive role in regulating alfalfa response to PEG-simulated drought stress, which might involve complex mechanisms, including ROS scavenging system, stomatal development and multiple phytohormone signaling pathways. This study will broaden our view on the function of γ-TMT gene and provide new strategy for genetic engineering in alfalfa breeding.
A cardiovascular disease risk factor in children with congenital heart disease: unmasking elevated waist circumference - a CHAMPS* study *CHAMPS: Children’s Healthy-Heart Activity Monitoring Program in Saskatchewan
Authors: Barbour-Tuck Erin , Boyes Natasha G. , Tomczak Corey R. , Lahti Dana S. , Baril Chantelle L. , Pockett Charissa , Runalls Shonah , Kakadekar Ashok , Pharis Scott , Bradley Timothy J. , Wright Kristi D. , Erlandson Marta C. 
Published: May 2020

Abstract
Background
Children with congenital heart disease (CHD) have an elevated risk of future cardiovascular disease but the underlying mechanisms are unclear. Abdominal obesity (measured as waist circumference) is a risk factor for adult onset of cardiovascular diseases and is correlated with low physical activity levels, commonly found in children with congenital heart disease. Elevated waist circumference may be a mechanism by which cardiovascular disease risk is elevated in children with CHD. The purpose of this study was to compare waist circumference between children with and without CHD, while considering potential confounders. We hypothesized that children with CHD would have higher measures of waist circumference when controlling for differences in birthweight, lean mass, and physical activity.

Methods
Thirty-two children with CHD (10.9 ± 2.6 years; 12 female) from the Children’s Healthy-Heart Activity Monitoring Program in Saskatchewan, and 23 healthy controls (11.7 ± 2.5 years; 10 female) were studied. Waist circumference, physical activity (physical activity questionnaire), body composition (lean mass; dual x-ray absorptiometry), and birthweight were assessed. Analysis of covariance, Mann-Whitney U, and independent sample t-tests were used to assess group differences (p < 0.05).

Results
Children with CHD had greater waist circumference than controls, controlling for lean mass, physical activity, birthweight, and sex (F (1, 49) = 4.488, p = 0.039). Physical activity, lean mass, and birthweight were not significantly different between groups (p > 0.05).

Conclusion
Our findings generate a novel hypothesis—higher waist circumferences in children with CHD compared to age-matched controls, may contribute to an elevated risk of cardiovascular disease.
Takotsubo cardiomyopathy and pituitary apoplexy: a case report
Authors: Yang Chun , Han Xiu , Du Yuan , Ma Ai-qun 
Published: May 2020

Abstract
Background
Takotsubo cardiomyopathy (TTC) has been widely recognized in recent decades and is triggered by either physical or psychological stressors.

Case presentation
A 70-year-old woman presented to the Emergency Department due to confusion, hypotension, fever, chills, and cough. She had a one-year history of diabetes insipidus. Pituitary function examination at admission revealed decreased thyroid, sex and adrenal hormones. Pituitary MRI displayed findings suggestive of nonhemorrhagic pituitary apoplexy. Electrocardiogram (ECG) revealed T-wave inversion and extended QT interval. Transthoracic echocardiogram (TTE) showed left ventricular apical dysplasia and ballooning, accompanied by reduced left ventricular ejection fraction. Coronary angiography (CAG) revealed no obvious coronary arterial stenosis. The left ventriculogram demonstrated an octopus clathrate appearance. Most ECG and TTE changes recovered 10 days later.

Conclusions
To the best of our knowledge, this is the first report of newly diagnosed TTC associated with pituitary apoplexy.
Diagnostic uncertainty and urinary tract infection in the emergency department: a cohort study from a UK hospital
Authors: Shallcross Laura J. , Rockenschaub Patrick , McNulty David , Freemantle Nick , Hayward Andrew , Gill Martin J. 
Published: May 2020

Abstract
Background
Suspected urinary tract infection (UTI) syndromes are a common reason for empirical antibiotics to be prescribed in the Emergency Department (ED), but differentiating UTI from other conditions with a similar presentation is challenging. We investigated how often an ED diagnosis of UTI is confirmed clinically/microbiologically, and described conditions which present as UTI syndromes.

Methods
Observational study using electronic health records from patients who attended the ED with suspected UTI and had a urine sample submitted for culture. We compared the ED diagnosis to diagnosis at discharge from hospital (ICD-10 codes), and estimated the proportion of cases with clinical/microbiological evidence of UTI.

Results
Two hundred eighty nine patients had an ED diagnosis of UTI syndrome comprising: lower UTI (191), pyelonephritis (56) and urosepsis (42). In patients admitted to hospital with an ED diagnosis of lower UTI, pyelonephritis or urosepsis, clinical/microbiological evidence of UTI was lacking in 61/103, 33/54 and 31/42 cases respectively. The ED diagnosis was concordant with the main reason for admission in less than 40% of patients with UTI syndromes, and antibiotics were stopped within 72 h in 37/161 patients.

Conclusions
Clinical/microbiological evidence of UTI was lacking in 60–70% of patients, suggesting scope to revise empirical prescribing decisions for UTI syndromes in light of microbial culture and clinical progression.
Fuzzy cognitive mapping and soft models of indigenous knowledge on maternal health in Guerrero, Mexico
Authors: Sarmiento Ivan , Paredes-Solís Sergio , Loutfi David , Dion Anna , Cockcroft Anne , Andersson Neil 
Published: May 2020

AbstractBackgroundEffective health care requires services that are responsive to local needs and contexts. Achieving this in indigenous settings implies communication between traditional and conventional medicine perspectives. Adequate interaction is especially relevant for maternal health because cultural practices have a notable role during pregnancy, childbirth and the postpartum period. Our work with indigenous communities in the Mexican state of Guerrero used fuzzy cognitive mapping to identify actionable factors for maternal health from the perspective of traditional midwives.MethodsWe worked with twenty-nine indigenous women and men whose communities recognized them as traditional midwives. A group session for each ethnicity explored risks and protective factors for maternal health among theMe’phaaandNancue ñomndaamidwives. Participants mapped factors associated with maternal health and weighted the influence of each factor on others. Transitive closure summarized the overall influence of each node with all other factors in the map. Using categories set in discussions with the midwives, the authors condensed the relationships with thematic analysis. The composite map combined categories in theMe’phaaand theNancue ñomndaamaps.ResultsTraditional midwives in this setting attend to pregnant women’s physical, mental, and spiritual conditions and the corresponding conditions of their offspring and family. The maps described a complex web of cultural interpretations of disease – “frío” (cold or coldness of the womb), “espanto” (fright), and “coraje” (anger) – abandonment of traditional practices of self-care, women’s mental health, and gender violence as influential risk factors. Protective factors included increased male involvement in maternal health (having a caring, working, and loving husband), receiving support from traditional healers, following protective rituals, and better nutrition.ConclusionsThe maps offer a visual language to present and to discuss indigenous knowledge and to incorporate participant voices into research and decision making. Factors with higher perceived influence in the eyes of the indigenous groups could be a starting point for additional research. Contrasting these maps with other stakeholder views can inform theories of change and support co-design of culturally appropriate interventions.
Early differential diagnosis of ankylosing spondylitis among patients with low back pain in primary care
Authors: Riis A. , Olesen J. L. , Thomsen J. L. 
Published: May 2020

AbstractDiagnosing and treating low back pain (LBP) is a worldwide major primary care challenge in which a differential diagnosis between non-specific LBP and conditions with a known pathology is essential for choosing the optimal treatment strategy. The time required for the diagnosis of a condition such as ankylosing spondylitis (AS) was previously found too long. However, a recently published paper by Bashir et al. found that distinct episodes of axial pain separated by more than 6 months seem more predictive than currently applied characteristics in reaching an early diagnosis of AS.
Unusual subdural empyema in a homeless patient diagnosed by molecular approach: a case report
Authors: Brin Cécile , Sougakoff Wladimir , Bielle Franck , Abi Jaoude Samya , Bonnet Isabelle , Haddad Elie , Caumes Eric , Jauréguiberry Stéphane 
Published: May 2020

Abstract
Background
We report a case of subdural empyema in a homeless patient caused by Bartonella quintana. B. quintana is a facultative intracellular bacteria for which bacterial growth is fastidious. The molecular biology approach has been a real help in establishing the diagnosis.

Case report
A 59-years old homeless patient, with a history of chronic alcohol abuse, was brought to the emergency department with a massive subdural empyema. Extensive microbiological evaluation didn’t reveal any pathogen in the pus collected before antibiotic treatment. B. quintana was detected in the pus from the empyema using a 16S rRNA-based PCR. Histology of intraoperative samples was consistent with the diagnosis and a serological assay was positive. The patient responded well to a treatment that included craniectomy with drainage of the loculated pus, total removal of the infected capsule and a combination of antibiotics.

Conclusion
This unique case of B. quintana-related empyema illustrates the risk of secondary infection of subdural hematoma with B. quintana since such infections have recently reemerged, predominantly among the homeless populations. Patients with subdural empyema in at-risk populations should be systematically evaluated for B. quintana with an appropriate diagnostic approach involving molecular biology.