bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal analysis of mRNA expression profiles in Orientia infected C3HeB/FeJ mouse
Authors: Chao Chien-Chung , Yang Ruoting , Zhang Zhiwen , Belinskaya Tatyana , Chan Chye-Teik , Miller Stacy-Ann , Hammamieh Rasha , Jett Marti , Ching Wei-Mei 
Published: January 2020

AbstractBackgroundScrub typhus causes up to 35% mortality if left untreated. One billion people living in the endemic regions are at risk. In spite of its heavy disease burden in some of the most populated areas in the world, there is no vaccine available. Although the disease can be effectively treated by proper antibiotics, timely and accurate diagnosis remains a challenge.Orientia tsutsugamushiinfects a variety of mammalian cells in vitro and replicates in the cytoplasm of the infected cells. Microarray analysis has been used extensively to study host-pathogen interactions in in vitro models to understand pathogenesis. However there is a lack of in vivo studies.ResultsIn this study, C3HeB/FeJ (C3H) mice were infected byO. tsutsugamushivia the intraperitoneal route and monitored gene expression at 10 different time points post infection. We observed two distinct types of expression profiles in the genes that we analyzed. There are two valleys (4–18 h and 2–4 days) with low number of differentially expressed genes (DEG) with three peaks with high number of DEG at 2 h, 1-day and 7-day post infection. Further analysis revealed that pathways like complement and coagulation cascade, and blood clotting cascade pathways showed significant global changes throughout entire time course. Real time quantitative Polymerase Chain Reaction (RT-qPCR) confirmed the change of expression for genes involved in complement and coagulation cascade. These results suggested dynamic regulation of the complement and coagulation cascades throughout most of the time post infection while some other specific pathways, such as fatty acid metabolism and tryptophan metabolism, are turned on or off at certain times post infection.ConclusionsThe findings highlight the complex interconnection among all different biological pathways. It is conceivable that specific pathways such as cell growth control and cell development in the host are affected byOrientiain the initial phase of infection forOrientiato grow intracellularly. OnceOrientiais replicating successfully inside the host as infection progresses, the infection could activate pathways involved in cellular immune responses to defend for host cell survival and try to eliminate the pathogen.
Cytological observation of anther structure and genetic investigation of a thermo-sensitive genic male sterile line 373S in Brassica napus L
Authors: Sun Yanyan , Zhang Dongsuo , Wang Zhenzhen , Guo Yuan , Sun Xiaomin , Li Wei , Zhi Wenliang , Hu Shengwu 
Published: January 2020

AbstractBackgroundPhotoperiod and/or thermo-sensitive male sterility is an effective pollination control system in crop two-line hybrid breeding. We previously discovered the spontaneous mutation of a partially male sterile plant and developed a thermo-sensitive genic male sterile (TGMS) line 373S inBrassica napusL. The present study characterized this TGMS line through cytological observation, photoperiod/ temperature treatments, and genetic investigation.ResultsMicroscopic observation revealed that the condensed cytoplasm and irregular exine of microspores and the abnormal degradation of tapetum are related to pollen abortion. Different temperature and photoperiod treatments in field and growth cabinet conditions indicated that the fertility alteration of 373S was mainly caused by temperature changes. The effects of photoperiod and interaction between temperature and photoperiod were insignificant. The critical temperature leading to fertility alteration ranged from 10 °C (15 °C/5 °C) to 12 °C (17 °C/7 °C), and the temperature-responding stage was coincident with anther development from pollen mother cell formation to meiosis stages. Genetic analysis indicated that the TGMS trait in 373S was controlled by one pair of genes, with male sterility as the recessive. Multiplex PCR analysis revealed that the cytoplasm of 373S ispoltype.ConclusionsOur study suggested that the 373S line inB. napushas a novel thermo-sensitive geneBnmst1inPolCMS cytoplasm background, and its fertility alteration is mainly caused by temperature changes. Our results will broaden the TGMS resources and lay the foundation for two-line hybrid breeding inB. napus.
Transcriptomic and metabolomic analysis reveals the role of CoA in the salt tolerance of Zygophyllum spp
Authors: Wang Jie , Jiang Xi , Zhao Chufeng , Fang Zhongming , Jiao Peipei 
Published: January 2020

AbstractBackgroundZygophyllumis an important medicinal plant, with notable properties such as resistance to salt, alkali, and drought, as well as tolerance of poor soils and shifting sand. However, the response mechanism ofZygophyllumspp. to abiotic stess were rarely studied.ResultsHere, we aimed to explore the salt-tolerance genes ofZygophyllumplants by transcriptomic and metabolic approaches. We choseZ. brachypterum,Z. obliquumandZ. fabagoto screen for salt tolerant and sensitive species. Cytological observation showed that both the stem and leaf ofZ. brachypterumwere significantly thicker than those ofZ. fabago.Then, we treated these three species with different concentrations of NaCl, and found thatZ. brachypterumexhibited the highest salt tolerance (ST), whileZ. fabagowas the most sensitive to salt (SS). With the increase of salt concentration, the CAT, SOD and POD activity, as well as proline and chlorophyll content in SS decreased significantly more than in ST. After salt treatment, the proportion of open stomata in ST decreased significantly more than in SS, although there was no significant difference in stomatal number between the two species. Transcriptomic analysis identified a total of 11 overlapping differentially expressed genes (DEGs) in the leaves and roots of the ST and SS species after salt stress. Two branched-chain-amino-acid aminotransferase (BCAT) genes among the 11 DEGs, which were significantly enriched in pantothenate and CoA biosynthesis, as well as the valine, leucine and isoleucine biosynthesis pathways, were confirmed to be significantly induced by salt stress through qRT-PCR. Furthermore, overlapping differentially abundant metabolites showed that the pantothenate and CoA biosynthesis pathways were significantly enriched after salt stress, which was consistent with the KEGG pathways enriched according to transcriptomics.ConclusionsIn our study, transcriptomic and metabolomic analysis revealed that BCAT genes may affect the pantothenate and CoA biosynthesis pathway to regulate the salt tolerance ofZygophyllumspecies, which may constitute a newly identified signaling pathway through which plants respond to salt stress.
Intensely clustered outbreak of visceral leishmaniasis (kala-azar) in a setting of seasonal migration in a village of Bihar, India
Authors: Kumar Arvind , Saurabh Suman , Jamil Sarosh , Kumar Vijay 
Published: January 2020

Abstract
Background
A visceral leishmaniasis outbreak was reported from a village in a low-endemic district of Bihar, India.

Methods
Outbreak investigation with house-to-house search and rapid test of kala-azar suspects and contacts was carried out. Sandfly collection and cone bio-assay was done as part of entomological study.

Results
A spatially and temporally clustered kala-azar outbreak was found at Kosra village in Sheikhpura district with 70 cases reported till December 2018. Delay of more than a year was found between diagnosis and treatment of the index case. The southern hamlet with socio-economically disadvantaged migrant population was several times more affected than rest of the village (attack rate of 19.0% vs 0.5% respectively, ORMH = 39.2, 95% CI 18.2–84.4). The median durations between onset of fever to first contact with any health services, onset to kala-azar diagnosis, diagnosis to treatment were 10 days (IQR 4–18), 30 days (IQR 17–73) and 1 day (IQR 0.5 to 3), respectively, for 50 kala-azar cases assessed till June 2017. Three-fourths of these kala-azar cases had out-of-pocket medical expenditure for their condition. Known risk factors for kala-azar such as illiteracy, poverty, belonging to socially disadvantaged community, migration, residing in kutcha houses, sleeping in rooms with unplastered walls and non-use of mosquito nets were present in majority of these cases. Only half the dwellings of the kala-azar cases were fully sprayed. Fully gravid female P. argentipes collected post indoor residual spraying (IRS) and low sandfly mortality on cone-bioassay indicated poor effectiveness of vector control.

Conclusions
There is need to focus on low-endemic areas of kala-azar. The elimination programme should implement a routine framework for kala-azar outbreak response. Complete case-finding, use of quality-compliant insecticide and coverage of all sprayable surfaces in IRS could help interrupt transmission during outbreaks.
ELISA is superior to bacterial culture and agglutination test in the diagnosis of brucellosis in an endemic area in China
Authors: Xu Nannan , Wang Wei , Chen Fengzhe , Li Wen , Wang Gang 
Published: January 2020

Abstract
Background
Brucellosis is endemic in many areas in China. The current diagnosis of Brucellosis predominantly relies on the traditional bacterial culture and serum agglutination test. In this study, we aimed to explore the value of ELISA in the diagnosis of Brucellosis in Chinese population.

Methods
We recruited 235 patients with a diagnosis of Brucellosis at different clinical stages: 117 in acute, 78 in subacute, and 40 in chronic. We also recruited 248 control patients who presented with similar clinical symptoms but with a different diagnosis other than Brucellosis. In addition, 90 healthy volunteers were also recruited. Bacterial culture, agglutination test and ELISA assay were performed to detect Brucella spp.

Results
Among 235 patients with Brucellosis, 51 (21.7%) was positive for bacterial culture, 150 (63.8%) were positive by agglutination test, and 232 (98.7%) were positive by ELISA (IgG and/or IgM). When we stratified the patients based on the disease stages (acute, subacute and chronic), ELISA was the most sensitive method and showed a highest positive rate in all stages. By Receiver Operating Characteristic Curve analysis of ELISA results, we found that measurement of IgG level was superior to measurement of IgM level (AUC, 0.993 versus 0.877). Since the measurement of IgG itself missed rare cases in acute phase, we recommended measuring IgG and IgM simultaneously by ELISA for the diagnosis of Brucellosis. In term of the specificity of ELISA in the diagnosis of Brucellosis, our study showed that only 1.6% (4/248) non-Brucellosis patients were positive by ELISA; all positive cases were IgM only and none showed positive IgG. Similar results were found in healthy volunteers. In summary, our study concluded that ELISA is the most sensitive and specific method to detect Brucellosis in Chinese population.

Conclusions
ELISA assay is sensitive, fast, and convenient to detect Brucellosis. It shows the high sensitivity and specifity and should be used as a routine lab test when Brucellosis is suspected in clinical practice.
Xpert MTB/RIF assay for diagnosis of extrapulmonary tuberculosis in children: a systematic review and meta-analysis
Authors: Seo Young Seok , Kang Ji-Man , Kim Dong Soo , Ahn Jong Gyun 
Published: January 2020

Abstract
Background
The Xpert® MTB/RIF assay (Xpert; Cepheid, Sunnyvale, CA, USA) is a cartridge-based nucleic acid amplification assay for rapidly diagnosing tuberculosis and assessing antibiotic sensitivity. Although previous evidence supports the use of Xpert for diagnosing extrapulmonary tuberculosis (EPTB) in adults, information regarding the accuracy of Xpert for EPTB only in children is lacking. This meta-analysis was performed to assess the accuracy of Xpert for detecting EPTB in children.

Methods
We searched the MEDLINE, EMBASE, and Cochrane Infectious Diseases Group Specialized Register from January 1, 2010 to July 16, 2019 for studies of the diagnostic performance wherein Xpert was analyzed against cultures or composite reference standards for < 18-year-old children with EPTB.

Results
In only pediatric studies, 8 studies including 652 samples were selected. The pooled sensitivity and specificity of Xpert for all samples were 71% (95% CI 0.63–0.79) and 97% (95% CI 0.95–0.99), respectively. The area under the summary receiver operating characteristic (sROC) curve was 0.89. For lymph node tissues or aspirates, the pooled sensitivity and specificity of Xpert were 80% (95% CI 0.70–0.88) and 94% (95% CI 0.89–0.97), respectively; for cerebrospinal fluid (CSF), these values were 42% (95% CI 0.22–0.63) and 99% (95% CI 0.95–1.00), respectively.

Conclusion
Overall, Xpert displayed high specificity but modest sensitivity across various samples for diagnosing pediatric EPTB compared to the composite reference standard. Xpert sensitivity varied with the sampling site and was especially lower in CSF samples. Positive Xpert results may be considered to indicate a presumptive case of pediatric EPTB, whereas negative test results indicate that the possibility of pediatric EPTB should not be excluded.
Survival of a case of Bacillus cereus meningitis with brain abscess presenting as immune reconstitution syndrome after febrile neutropenia – a case report and literature review-
Authors: Koizumi Yusuke , Okuno Takafumi , Minamiguchi Hitoshi , Hodohara Keiko , Mikamo Hiroshige , Andoh Akira 
Published: January 2020

Abstract
Background
Bacillus cereus sometimes causes central nervous system infection, especially in compromised hosts. In cases of meningitis arising during neutropenia, CSF abnormalities tend to be subtle and can be easily overlooked, and mortality rate is high. We report a survived case of B. cereus meningitis/brain abscess in severe neutropenia, presenting as immune reconstitution syndrome.

Case presentation
A 54-year-old Japanese female with acute myelogenous leukemia developed B. cereus bacteremia and meningitis during consolidation chemotherapy. At the onset, she presented with mild meningism. She had marked leukocytopenia (WBC <100/μL, neutrophils 0/μL) and lumbar puncture yielded only mild pleocytosis. She was transferred to intensive care unit, and meropenem, linezolid and vancomycin was started. With intensive therapy, she recovered and once became afebrile. On day 19, however, her fever, meningism and consciousness level dramatically worsened despite recovery of bone marrow function. The antimicrobial chemotherapy was continued and finally she was cured with no complications.

Conclusions
With early diagnosis and prompt initiation and of antibiotics, the case was successfully treated without any sequelae. It is important to remember that, even under optimal antimicrobial therapy, bone marrow recovery can cause transient reaggravation of the disease. In such cases, timely and appropriate evaluation should be done to make the clinical decision to change, continue, or intensify treatment.
Alpha and beta-Thalassemia mutations in Hubei area of China
Authors: Zhu Yaowu , Shen Na , Wang Xiong , Xiao Juan , Lu Yanjun 
Published: January 2020

Abstract
Background
Thalassemia is a group of inherited hemoglobic disorders resulting from defects
in the synthesis of one or more of the hemoglobin chains, which is one of the most prevalent inherited disorders in southern China. Only few studies reported the molecular characterization of α- and β-Thalassemia in Hubei Province in the central of China.

Methods
A total of 4889 clinically suspected cases of thalassemia were analyzed by Gap-PCR, PCR-based reverse dot blot (RDB).

Results
1706 (33.8%) subjects harbored thalassemia mutations, including 539 (11.0%) subjects with α-thalassemia, 1140 (23.3%) subjects with β-thalassemia mutations, and 25 (0.51%) subjects with both α- and β-thalassemia mutations. Seven genotypes of α-thalassemia mutations and 29 genotypes of β-thalassemia mutations were characterized. --SEA/αα (66.05%), −α3.7/αα (24.12%), and -α4.2/αα (3.71%) accounted for 93.88% of the α-thalassemia mutations. βIVS-II-654/βN, βCD41–42/βN, βCD17/βN, βCD27–28/βN, βCD71–72/βN, β − 28/βN, β − 29/βN, βCD43/βN, βE/βN, accounting for 96.40% of all β-thalassemia genotypes. Furthermore, mean corpuscular volume (MCV) and mean corpuscular Hb (MCH) were sensitive markers for both β-thalassemia and α-thalassemia with --SEA/αα, but not -α3.7/αα and -α4.2/αα. Conclusions: Our data indicated great heterogeneity and extensive spectrum of thalassemias in Hubei province of China.
Dual kidney transplantation offers a safe and effective way to use kidneys from deceased donors older than 70 years
Authors: Lee Kyo Won , Park Jae Berm , Cha So Ra , Lee Seo Hee , Chung Young Jae , Yoo Heejin , Kim Kyunga , Kim Sung Joo 
Published: January 2020

AbstractPurposeDual kidney transplantation (DKT) offers a way to extend the use of kidneys from expanded criteria donors (ECDs). Here, we compared the outcomes of DKT with those of single kidney transplantation from standard criteria donors (SCDs) and ECDs.MethodsIn 2014, we began performing DKT using both kidneys from deceased donors greater than 70 years of age with one of two risk factors: serum creatinine (sCr) level over 3.0 mg/dl or eGFR under 30 ml/min. By 2017, we had performed 15 DKTs. We compared the outcomes of the 15 DKT recipients with those of 124 patients who received a kidney from an SCD and 80 patients who received a kidney from an ECD.ResultsCompared with ECDs and SCDs, DKT donors were older, had a higher diabetes burden, and a higher sCr level (p < 0.01, < 0.01, and 0.03, respectively). DKT recipients were also older and had a higher diabetes burden than recipients of kidneys from ECDs and SCDs (p < 0.01, both). DKT recipients had a lower nadir sCr and shorter duration to nadir sCr than single ECD KT recipients (p < 0.01and 0.04, respectively).ConclusionsThe survival rates of DKT grafts were compatible with those of single KT grafts. Therefore, DKT may be considered a suitable an option to expand the donor pool.
Impact of the donor-recipient gender matching on the graft survival from live donors
Authors: Naderi Gholamhossein , Azadfar Amin , Yahyazadeh Seyed Reza , Khatami Fatemeh , Aghamir Seyed Mohammad Kazem 
Published: January 2020

AbstractBackgroundSeveral factors such as recipient age, BMI, serum cratinine, and positive history of dialysis are important in predicting graft survival among kidney transplant recipients. One factor affecting the transplant outcomes is donors and recipients gender, which is usually ignored.MethodsA total of 1113 kidney transplant recipients were studied in this retrospective cohort study. Several factors were taken into account for graft survival and outcomes such as donors and recipients gender and age in addition to common recipient factors like cratinine, eGFR, BMI, and positive history of dialysis.ResultsThe most successful transplant based on donor-recipient gender was observed in male donor to male recipient, and then male donor to female recipient. In female transplant recipients, level of serum cratinine and eGFR, positive dialysis history before transplant, and low donor hemoglobin level can be considered as good prognostic factors recommended for kidney transplant survival.ConclusionsOur results suggested gender matching for kidney transplant. Only in some exceptional conditions, male donor to female recipient kidney transplant may be successful and female donors to male recipients are not suggested, especially in aged patients with the history of dialysis.
Associations between the measures of physical function, risk of falls and the quality of life in haemodialysis patients: a cross-sectional study
Authors: Vanden Wyngaert Karsten , Van Craenenbroeck Amaryllis H. , Eloot Sunny , Calders Patrick , Celie Bert , Holvoet Els , Van Biesen Wim 
Published: January 2020

Abstract
Background
Impaired physical function due to muscle weakness and exercise intolerance reduces the ability to perform activities of daily living in patients with end-stage kidney disease, and by consequence, Health-Related Quality of Life (HRQoL). Furthermore, the risk of falls is an aggregate of physical function and, therefore, could be associated with HRQoL as well. The present study examined the associations between objective and subjective measures of physical function, risk of falls and HRQoL in haemodialysis patients.

Methods
This cross-sectional multicentre study included patients on maintenance haemodialysis. Physical function (quadriceps force, handgrip force, Sit-to-Stand, and six-minute walking test), the risk of falls (Tinetti, FICSIT-4, and dialysis fall index) and HRQoL (PROMIS-29 and EQ-5D-3 L) were measured and analysed descriptively, by general linear models and logistic regression.

Results
Of the 113 haemodialysis patients (mean age 67.5 ± 16.1, 57.5% male) enrolled, a majority had impaired quadriceps force (86.7%) and six-minute walking test (92%), and an increased risk of falls (73.5%). Whereas muscle strength and exercise capacity were associated with global HRQoL (R2 = 0.32) and the risk of falls, the risk of falls itself was related to psycho-social domains (R2 = 0.11) such as depression and social participation, rather than to the physical domains of HRQoL. Objective measures of physical function were not associated with subjective fatigue, nor with subjective appreciation of health status.

Conclusions
More than muscle strength, lack of coordination and balance as witnessed by the risk of falls contribute to social isolation and HRQoL of haemodialysis patients. Mental fatigue was less common than expected, whereas, subjective and objective physical function were decreased.
Major obstetric haemorrhage in Metro East, Cape Town, South Africa: a population-based cohort study using the maternal near-miss approach
Authors: Heitkamp Anke , Aronson Simcha Lot , van den Akker Thomas , Vollmer Linda , Gebhardt Stefan , van Roosmalen Jos , de Vries Johanna I. , Theron Gerhard 
Published: January 2020

Abstract
Background
Major obstetric haemorrhage is a leading cause of maternal mortality and accounts for one-third of maternal deaths in of Africa. This study aimed to assess the population-based incidence, causes, management and outcomes of major obstetric haemorrhage and risk factors associated with poor maternal outcome.

Methods
Women with major obstetric haemorrhage who met the WHO maternal near-miss criteria or died in the Metro East region, Cape Town, South Africa, were evaluated from November 2014–November 2015. Major obstetric haemorrhage was defined as haemorrhage in pregnancies of at least 20 weeks’ gestation or occurring up to 42 days after birth, and leading to hysterectomy, hypovolaemic shock or blood transfusion of ≥5 units of Packed Red Blood Cells. A logistic regression model was used to analyse associations with poor outcome, defined as major obstetric haemorrhage leading to massive transfusion of ≥8 units of packed red blood cells, hysterectomy or death.

Results
The incidence of major obstetric haemorrhage was 3/1000 births, and the incidence of massive transfusion was 4/10.000 births in the Metro East region (32.862 births occurred during the studied time period). Leading causes of haemorrhage were placental abruption 45/119 (37.8%), complications of caesarean section 29/119 (24.4%) and uterine atony 13/119 (10.9%). Therapeutic oxytocin was administered in 98/119 (82.4%) women and hysterectomy performed in 33/119 (27.7%). The median numbers of packed red blood cells and units of Fresh Frozen Plasma transfused were 6 (interquartile range 4–7) and 3 (interquartile range 2–4), ratio 1.7:1. Caesarean section was independently associated with poor maternal outcome: adjusted OR 4.01 [95% CI 1.58, 10.14].

Conclusions
Assessment of major obstetric haemorrhage using the Maternal Near Miss approach revealed that placental abruption and complications of caesarean section were the major causes of major obstetric haemorrhage. Caesarean section was associated with poor outcome.