bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effects of a globin blocker on the resolution of 3’mRNA sequencing data in porcine blood
Authors: Lim Kyu-Sang , Dong Qian , Moll Pamela , Vitkovska Jana , Wiktorin Gregor , Bannister Stephanie , Daujotyte Dalia , Tuggle Christopher K. , Lunney Joan K. , Plastow Graham S. , Dekkers Jack C. M. 
Published: October 2019

Abstract

Background
Gene expression profiling in blood is a potential source of biomarkers to evaluate or predict phenotypic differences between pigs but is expensive and inefficient because of the high abundance of globin mRNA in porcine blood. These limitations can be overcome by the use of QuantSeq 3’mRNA sequencing (QuantSeq) combined with a method to deplete or block the processing of globin mRNA prior to or during library construction. Here, we validated the effectiveness of QuantSeq using a novel specific globin blocker (GB) that is included in the library preparation step of QuantSeq.

Results
In data set 1, four concentrations of the GB were applied to RNA samples from two pigs. The GB significantly reduced the proportion of globin reads compared to non-GB (NGB) samples (P = 0.005) and increased the number of detectable non-globin genes. The highest evaluated concentration (C1) of the GB resulted in the largest reduction of globin reads compared to the NGB (from 56.4 to 10.1%). The second highest concentration C2, which showed very similar globin depletion rates (12%) as C1 but a better correlation of the expression of non-globin genes between NGB and GB (r = 0.98), allowed the expression of an additional 1295 non-globin genes to be detected, although 40 genes that were detected in the NGB sample (at a low level) were not present in the GB library. Concentration C2 was applied in the rest of the study. In data set 2, the distribution of the percentage of globin reads for NGB (n = 184) and GB (n = 189) samples clearly showed the effects of the GB on reducing globin reads, in particular for HBB, similar to results from data set 1. Data set 3 (n = 84) revealed that the proportion of globin reads that remained in GB samples was significantly and positively correlated with the reticulocyte count in the original blood sample (P < 0.001).

Conclusions
The effect of the GB on reducing the proportion of globin reads in porcine blood QuantSeq was demonstrated in three data sets. In addition to increasing the efficiency of sequencing non-globin mRNA, the GB for QuantSeq has an advantage that it does not require an additional step prior to or during library creation. Therefore, the GB is a useful tool in the quantification of whole gene expression profiles in porcine blood.
Selection of candidate genes controlling veraison time in grapevine through integration of meta-QTL and transcriptomic data
Authors: Delfino Pietro , Zenoni Sara , Imanifard Zahra , Tornielli Giovanni Battista , Bellin Diana 
Published: October 2019

AbstractBackgroundHigh temperature during grape berry ripening impairs the quality of fruits and wines. Veraison time, which marks ripening onset, is a key factor for determining climatic conditions during berry ripening. Understanding its genetic control is crucial to successfully breed varieties more adapted to a changing climate. Quantitative trait loci (QTL) studies attempting to elucidate the genetic determinism of developmental stages in grapevine have identified wide genomic regions. Broad scale transcriptomic studies, by identifying sets of genes modulated during berry development and ripening, also highlighted a huge number of putative candidates.ResultsWith the final aim of providing an overview about available information on the genetic control of grapevine veraison time, and prioritizing candidates, we applied a meta-QTL analysis for grapevine phenology-related traits and checked for co-localization of transcriptomic candidates. A consensus genetic map including 3130 markers anchored to the grapevine genome assembly was compiled starting from 39 genetic maps. Two thousand ninety-three QTLs from 47 QTL studies were projected onto the consensus map, providing a comprehensive overview about distribution of available QTLs and revealing extensive co-localization especially across phenology related traits. From 141 phenology related QTLs we generated 4 veraison meta-QTLs located on linkage group (LG) 1 and 2, and 13 additional meta-QTLs connected to the veraison time genetic control, among which the most relevant were located on LG 14, 16 and 18. Functional candidates in these intervals were inspected. Lastly, taking advantage of available transcriptomic datasets, expression data along berry development were integrated, in order to pinpoint among positional candidates, those differentially expressed across the veraison transition.ConclusionIntegration of meta-QTLs analysis on available phenology related QTLs and data from transcriptomic dataset allowed to strongly reduce the number of candidate genes for the genetic control of the veraison transition, prioritizing a list of 272 genes, among which 78 involved in regulation of gene expression, signal transduction or development.
A leucine-rich repeat-receptor-like kinase gene SbER2–1 from sorghum (Sorghum bicolor L.) confers drought tolerance in maize
Authors: Li Hanshuai , Han Xiaodong , Liu Xinxiang , Zhou Miaoyi , Ren Wen , Zhao Bingbing , Ju Chuanli , Liu Ya , Zhao Jiuran 
Published: October 2019

Abstract

Background
ERECTA (ER) is a leucine-rich repeat-receptor-like kinase gene (LRR-RLK) encoding a protein isolated from Arabidopsis. Although the regulatory functions of ER genes have been widely explored in plant development and disease resistance, their roles in drought stress responses remain to be clarified.

Results
In this study, we cloned and characterized two ER genes, SbER1–1 and SbER2–1, from the drought-tolerant model plant sorghum (Sorghum bicolor L.). Under drought stress, the two genes were expressed in the leaves and stems but not in the roots, and SbER2–1 transcript accumulation in the stem was increased. SbER2–1 was localized both on the plasma membrane and in the chloroplast. Moreover, SbER2–1 expression in Arabidopsis and maize conferred increased drought tolerance, especially in regard to water-use efficiency, increasing the net photosynthetic rate in maize under drought stress. Based on RNA-Seq analysis together with the physiological data, we conclude that the transgenic maize plants have upregulated phenylpropanoid metabolism and increased lignin accumulation under drought stress.

Conclusions
Our results demonstrate that SbER2–1 plays an important role in response to drought stress. Furthermore, photosynthetic systems and phenylpropanoid metabolism are implicated in SbER2–1-mediated drought stress tolerance mechanisms. The use of genetic engineering to regulate SbER2–1 expression in plants and to breed new varieties tolerant to drought is a research field full of potential.
Short-term inhibition of glutamine synthetase leads to reprogramming of amino acid and lipid metabolism in roots and leaves of tea plant (Camellia sinensis L.)
Authors: Liu Mei-Ya , Tang Dandan , Shi Yuanzhi , Ma Lifeng , Li Yan , Zhang Qunfeng , Ruan Jianyun 
Published: October 2019

Abstract

Background
Nitrogen (N) nutrition significantly affected metabolism and accumulation of quality-related compounds in tea plant (Camellia sinensis L.). Little is known about the physiological and molecular mechanisms underlying the effects of short-term repression of N metabolism on tea roots and leaves for a short time.

Results
In this study, we subjected tea plants to a specific inhibitor of glutamine synthetase (GS), methionine sulfoximine (MSX), for a short time (30 min) and investigated the effect of the inhibition of N metabolism on the transcriptome and metabolome of quality-related compounds. Our results showed that GS activities in tea roots and leaves were significantly inhibited upon MSX treatment, and both tissue types showed a sensitive metabolic response to GS inhibition. In tea leaves, the hydrolysis of theanine decreased with the increase in theanine and free ammonium content. The biosynthesis of all other amino acids was repressed, and the content of N-containing lipids declined, suggesting that short-term inhibition of GS reduces the level of N reutilization in tea leaves. Metabolites related to glycolysis and the tricarboxylic acid (TCA) cycle accumulated after GS repression, whereas the content of amino acids such as glycine, serine, isoleucine, threonine, leucine, and valine declined in the MXS treated group. We speculate that the biosynthesis of amino acids is affected by glycolysis and the TCA cycle in a feedback loop.

Conclusions
Overall, our data suggest that GS repression in tea plant leads to the reprogramming of amino acid and lipid metabolic pathways.
Functional impairment and serum albumin predict in-hospital mortality in nonagenarians with acute infection: a retrospective cohort study
Authors: Huang Wei , Sun Ying , Xing Yunli , Wang Cuiying 
Published: October 2019

Abstract

Background
Acute infection leads to substantial mortality in the nonagenarian population. However, the predictive efficacies of functional status and biochemical indexes for in-hospital mortality in these patients remain to be determined.

Methods
A single-center, retrospective cohort study was performed. Consecutive nonagenarian patients who were admitted to our department from January 1, 2014 to December 31, 2016 for acute infectious diseases were included. Baseline data for medical history, functional status, and biochemical indexes were obtained on admission. The outcomes of these patients during hospitalization were recorded. Predictors of in-hospital mortality were identified via logistic regression analyses.

Results
A total of 162 patients were included, and 46 patients died (17.2%) during hospitalization. Univariate analysis showed that the prevalence rates of atrial fibrillation (32.1%) and malignant disease (26.5%) were higher in nonagenarian patients who died during hospitalization than in those who discharged. Multivariate logistic regression analyses identified malignant disease (odds ratio [OR] 2.73, 95% confidence interval [CI]: 1.10–6.78), ADL category (OR 0.82, 95% CI: 0.75–0.89) and serum albumin (OR 0.86, 95%CI 0.78–0.95) as independent predictors of in-hospital mortality in nonagenarian patients hospitalized for acute infection.

Conclusions
Functional impairment as well as serum albumin may be independent predictors of in-hospital mortality in nonagenarian patients hospitalized for acute infectious diseases. Stratification of patients according to Barthel Index score and serum albumin is very necessary.
Blood stream infections associated with central and peripheral venous catheters
Authors: Ruiz-Giardin Jose Manuel , Ochoa Chamorro Iciar , Velázquez Ríos Laura , Jaqueti Aroca Jeronimo , García Arata Maria Isabel , SanMartín López Juan Víctor , Guerrero Santillán Marta 
Published: October 2019

Abstract

Background
The purposes of this study were to determine the incidence of central and peripheral venous catheter-related bacteraemias, the relationship between the suspected and final confirmed bacteraemia origins, and the differences in microbiological, epidemiological, clinical, and analytical characteristics between the groups, including evolution to death.

Methods
This was a 7-year descriptive retrospective populational study of all bloodstream infections, comparing central (CB) and peripheral (PB) venous catheter-related bacteraemias in patients older than 15 years.

Results
In all, 285 catheter-related bacteraemia patients, 220 with CBs (77.19%) and 65 with PBs (22.81%), were analysed among 1866 cases with bloodstream infections. The cumulative incidence per 1000 patients-day of hospital stay was 0.36 for CB and 0.106 for PB.
In terms of the suspected origin, there was less accuracy in diagnosing catheter-related bloodstream infections (68. 2%) than those of other origins (78. 4%), p <  0.001. The accuracy was greater for PB (75%) than for CB (66. 2%),
Coagulase-negative staphylococci were the most frequent microorganisms in both groups but occurred 1.57 times more frequently in CB (64.1%/40.6%) (p = 0.004), while Staphylococcus aureus (23. 4%/9.5%) (p = 0.02) and Enterobacteriae species (15.6%/6. 3%) (p = 0.003) were 2.5 times more frequent in PB.
The CB patients stayed at the hospital for an average of 7.44 days longer than did the PB patients; more CB patients had active neoplasia (70. 4%/32.8%), more had surgery in the previous week (29. 2%/8. 3%), and fewer received adequate empirical treatment (53.9%/ 62.5%). Catheter was not removed in 8. 2% of CB and 3.7% of PB. On the other hand, the CB and PB patients had similar Pitt scores at blood extraction (median 0.89 versus 0.84 points, respectively; p = 0.8) and similar survival rates at hospital discharge (91.1% versus 90. 2%; p = 0.81).

Conclusions
Central catheters were more frequent sources of bacteraemias than were peripheral catheters. There were important differences in the microbiological aetiology as well. PB patients received correct empirical antibiotic treatment more frequently and had a higher initial rate of correct determination of the suspected source of bacteraemia. Differences in the microbiological aetiology and empirical antibiotic treatment received, and probably catheter removal and time to catheter removal could explain why CB and PB patients had similar survival rates .
Case report: chronic relapsing cryptococcal meningitis in a patient with low mannose-binding lectin and a low naïve CD4 cell count
Authors: Wagemakers Alex , Ang Cornelis Willem , Hagen Ferry , Bot Joost Cornelis Johannes , Bomers Marije Kristianne , Visser Marieke Christine , van Dijk Karin 
Published: October 2019

AbstractBackgroundCryptococcal meningitis is most commonly found in HIV-infected patients. In HIV-negative patients, its low incidence can lead to prolonged time to diagnosis. Detailed case reports of chronic cryptococcal meningitis are scarce, but could provide clues for earlier diagnosis in this patient category.Case presentationA 60-year old man presented June 2015 with intermittent headaches for several months without any fever. Initial work-up showed a leukocytosis, raised CSF opening pressure and raised leukocytes and protein in the CSF. An MRI revealed leptomeningeal contrast enhancement and cerebellar oedema. While malignancy and various infectious causes were excluded, the patient had a spontaneous clinical and radiological recovery. One year later, the patient returned with complaints of headaches. Also, cerebellar oedema and leptomeningeal contrast enhancement had recurred. Eventually in March 2017, the novel cryptococcal antigen lateral flow assay (CrAg LFA) was positive on CSF, and one colony ofCryptococcus neoformanswas cultured from CSF. The patient was treated with the standard antifungal regimen which resulted in resolution of his headaches. In retrospect, the cryptococcal antigen test was already positive on a serum sample from June 2015. Interestingly, post-treatment immunological analysis revealed both a low mannose-binding lectin (MBL) concentration and low naïve CD4 counts.ConclusionsWe present a patient with cryptococcal meningitis in an HIV-negative patient with low MBL and low naïve CD4 count suffering a chronic relapsing meningo-encephalitis with relatively mild symptoms for around 2 years. In patients with an unexplained meningo-encephalitis such as this case, early performance of CrAg LFA on serum and/or CSF is an inexpensive and rapid method to reduce time-to diagnosis.
Can apparent diffusion coefficient (ADC) distinguish breast cancer from benign breast findings? A meta-analysis based on 13 847 lesions
Authors: Surov Alexey , Meyer Hans Jonas , Wienke Andreas 
Published: October 2019

Abstract

Background
The purpose of the present meta-analysis was to provide evident data about use of Apparent Diffusion Coefficient (ADC) values for distinguishing malignant and benign breast lesions.

Methods
MEDLINE library and SCOPUS database were screened for associations between ADC and malignancy/benignancy of breast lesions up to December 2018. Overall, 123 items were identified. The following data were extracted from the literature: authors, year of publication, study design, number of patients/lesions, lesion type, mean value and standard deviation of ADC, measure method, b values, and Tesla strength.
The methodological quality of the 123 studies was checked according to the QUADAS-2 instrument. The meta-analysis was undertaken by using RevMan 5.3 software. DerSimonian and Laird random-effects models with inverse-variance weights were used without any further correction to account for the heterogeneity between the studies. Mean ADC values including 95% confidence intervals were calculated separately for benign and malign lesions.

Results
The acquired 123 studies comprised 13,847 breast lesions. Malignant lesions were diagnosed in 10,622 cases (76.7%) and benign lesions in 3225 cases (23.3%). The mean ADC value of the malignant lesions was 1.03 × 10− 3 mm2/s and the mean value of the benign lesions was 1.5 × 10− 3 mm2/s. The calculated ADC values of benign lesions were over the value of 1.00 × 10− 3 mm2/s. This result was independent on Tesla strength, choice of b values, and measure methods (whole lesion measure vs estimation of ADC in a single area).

Conclusion
An ADC threshold of 1.00 × 10− 3 mm2/s can be recommended for distinguishing breast cancers from benign lesions.
Prevalence of malarial recurrence and hematological alteration following the initial drug regimen: a retrospective study in Western Thailand
Authors: Kotepui Manas , Punsawad Chuchard , Kotepui Kwuntida Uthaisar , Somsak Voravuth , Phiwklam Nuoil , PhunPhuech Bhukdee 
Published: October 2019

Abstract

Background
The hematological changes following the initial drug regimen has been poorly understood in Thailand. This study was designed to determine the prevalence of malaria parasite recurrence and hematological alteration of patients during the initial drug regimen.

Methods
A retrospective study was conducted at Phop Phra Hospital, Tak Province, located in northwestern Thailand. All data from patients who were diagnosed with Plasmodium spp. infection – including types of Plasmodium spp., clinical characteristics, and hematological parameters – were retrieved and analyzed.

Results
The results demonstrated that during years 2012–2018, 95 out of 971 patients (9.78%) were infected with malaria two or more times. The gender, nationality, symptom of headache, type of Plasmodium spp., and career of each patient were associated with recurrence (P-value< 0.05). Among patients treated with malarial drug, the leukocyte count and red cell distribution width (RDW) were significantly changed when compared to untreated patients with recurrence (P-value< 0.05).

Conclusion
This study indicated the high prevalence of malarial recurrence in Tak Province, Western Thailand, and its relationship to certain characteristics of individuals. Patients who were treated with antimalarial drugs exhibited leukocyte and RDW changes following the initial drug regimen. This data could be useful for prompt detection, treatment, and prevention of malarial recurrence in endemic areas of Thailand.
Low-income community knowledge, attitudes and perceptions regarding antibiotics and antibiotic resistance in Jelutong District, Penang, Malaysia: a qualitative study
Authors: Irawati Lyna , Alrasheedy Alian A. , Hassali Mohamed Azmi , Saleem Fahad 
Published: October 2019

Abstract

Background
Understanding community perspectives on antibiotics and antibiotic resistance (ABR) is a key component in designing educational interventions to combat ABR at the community level in Malaysia. Therefore, this study aimed to explore community residents’ knowledge, attitudes and perceptions regarding antibiotics and ABR in Jelutong District, Penang, Malaysia. Moreover, it intended to identify areas of focus to be addressed when designing an educational intervention to increase residents’ knowledge and change their attitudes and perceptions.

Methods
A qualitative approach was adopted to gain a deeper understanding of community residents’ knowledge, attitudes and perceptions regarding antibiotics and ABR. A purposive sampling was employed. Twenty-two residents (aged ≥18 years) were interviewed with the aid of a semi-structured interview guide. All interviews were audio recorded, transcribed verbatim and thematically analysed.

Results
The majority of the participants asserted that antibiotics could be effective against viral infections. Moreover, many participants were unaware that antibiotics have adverse effects. Some acquired antibiotics from a community pharmacy without a prescription, took antibiotics given to them by their family or friends, or took leftover antibiotics prescribed for a previous illness. A few indicated that they would request antibiotics from their physician when they had viral infections. More than half of the participants discontinued taking antibiotics when their symptoms improved. The majority stated that ABR occurs when the body becomes used to antibiotics. Most participants were unaware of the causes, consequences and prevention of ABR. In fact, they were not concerned about it. As a result, only a few perceived themselves as having responsibility for preventing this problem.

Conclusions
The community residents had misconceptions about antibiotics and ABR, negative attitudes towards antibiotics and negative perceptions of ABR. The areas of focus that need to be addressed when designing an educational intervention to increase the general public knowledge and change their attitudes and perceptions are the appropriate use of antibiotics and their adverse effects; the importance of adhering to antibiotic therapy; and the definition, causes, consequences and prevention of ABR.
The influence of obesity and gender on outcome after reversed L-shaped osteotomy for hallux valgus
Authors: Wirth Stephan H. , Renner Niklas , Niehaus Richard , Farei-Campagna Jan , Deggeller Marcel , Scheurer Fabrice , Palmer Katie , Jentzsch Thorsten 
Published: October 2019

Abstract

Background
Hallux valgus deformity (HV) affects around every fourth individual, and surgical treatment is performed in every thousandth person. There is an ongoing quest for the best surgical management and reduction of undesirable outcomes. The aim was to explore associations of obesity and gender with radiological and clinical outcome after reversed L-shaped osteotomy (ReveL) for HV.

Materials and methods
This study was carried out in a retrospective cohort design at a single University Hospital in Switzerland between January 2004 and December 2013. It included adult patients treated with ReveL for HV. The primary exposure was body mass index (BMI) at the time of ReveL. The secondary exposure was gender. The primary outcome was radiological relapse of HV (HV angle [HVA] > 15 degrees [°]) at the last follow-up. Secondary outcomes were improvable patient satisfaction, complication, redo surgery, and optional hardware removal. Logistic regression analysis adjusted for confounders.

Results
The median weight, height, and BMI were 66.0 (interquartile range [IQR] 57.0–76.0) kilograms (kg), 1.65 (IQR 1.60–1.71) metres (m), and 24.0 (IQR 21.3–27.8) kg/m2. Logistic regression analysis did not show associations of relapse with BMI, independent of age, gender, additional technique, and preoperative HVA (adjusted odds ratio [ORadjusted] = 1.10 [95% (%) confidence interval (CI) = 0.70–1.45], p = 0.675). Relapse was 91% more likely in males (ORadjusted = 1.91 [95% CI = 1.19–3.06], p = 0.007). Improvable satisfaction was 79% more likely in males (ORadjusted = 1.79 [CI = 1.04–3.06], p = 0.035). Hardware removal was 47% less likely in males (ORadjusted = 0.53 [95% CI 0.30–0.94], p = 0.029).

Conclusions
In this study, obesity was not associated with unsatisfactory outcomes after ReveL for HV. This challenges the previous recommendation that preoperative weight loss may be necessary for a successful surgical treatment outcome. Males may be informed about potentially higher associations with unfavourable outcomes. Due to the risk of selection bias and lack of causality, findings may need to be confirmed with clinical trials.