bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network regression analysis in transcriptome-wide association studies
Authors: Jin Xiuyuan , Zhang Liye , Ji Jiadong , Ju Tao , Zhao Jinghua , Yuan Zhongshang 
Published: August 2022

Abstract
Background
Transcriptome-wide association studies (TWASs) have shown great promise in interpreting the findings from genome-wide association studies (GWASs) and exploring the disease mechanisms, by integrating GWAS and eQTL mapping studies. Almost all TWAS methods only focus on one gene at a time, with exception of only two published multiple-gene methods nevertheless failing to account for the inter-dependence as well as the network structure among multiple genes, which may lead to power loss in TWAS analysis as complex disease often owe to multiple genes that interact with each other as a biological network. We therefore developed a Network Regression method in a two-stage TWAS framework (NeRiT) to detect whether a given network is associated with the traits of interest. NeRiT adopts the flexible Bayesian Dirichlet process regression to obtain the gene expression prediction weights in the first stage, uses pointwise mutual information to represent the general between-node correlation in the second stage and can effectively take the network structure among different gene nodes into account.

Results
Comprehensive and realistic simulations indicated NeRiT had calibrated type I error control for testing both the node effect and edge effect, and yields higher power than the existed methods, especially in testing the edge effect. The results were consistent regardless of the GWAS sample size, the gene expression prediction model in the first step of TWAS, the network structure as well as the correlation pattern among different gene nodes. Real data applications through analyzing systolic blood pressure and diastolic blood pressure from UK Biobank showed that NeRiT can simultaneously identify the trait-related nodes as well as the trait-related edges.

Conclusions
NeRiT is a powerful and efficient network regression method in TWAS.
What is the best technic to dislodge Staphylococcus epidermidis biofilm on medical implants?
Authors: Moris Vivien , Lam Mylan , Amoureux Lucie , Magallon Arnaud , Guilloteau Adrien , Maldiney Thomas , Zwetyenga Narcisse , Falentin-Daudre Céline , Neuwirth Catherine 
Published: August 2022

Abstract
Background
Bacterial biofilm can occur on all medical implanted devices and lead to infection and/or dysfunction of the device.
In this study, artificial biofilm was formed on four different medical implants (silicone, piccline, peripheral venous catheter and endotracheal tube) of interest for our daily clinical and/or research practice. We investigated the best conventional technic to dislodge the biofilm on the implants and quantified the number of bacteria. Staphylococcus epidermidis previously isolated from a breast implant capsular contracture on a patient in the university hospital of Dijon was selected for its ability to produce biofilm on the implants. Different technics (sonication, Digest-EUR®, mechanized bead mill, combination of sonication plus Digest-EUR®) were tested and compared to detach the biofilm before quantifying viable bacteria by colony counting.

Results
For all treatments, the optical and scanning electron microscope images showed substantial less biofilm biomass remaining on the silicone implant compared to non-treated implant.
This study demonstrated that the US procedure was statistically superior to the other physical treatment: beads, Digest-EUR® alone and Digest-EUR® + US (p < 0.001) for the flexible materials (picc-line, PIV, and silicone). The number of bacteria released by the US is significantly higher with a difference of 1 log on each material. The result for a rigid endotracheal tube were different with superiority for the chemical treatment dithiothreitol: Digest-EUR®. Surprisingly the combination of the US plus Digest-EUR® treatment was consistently inferior for the four materials.

Conclusions
Depending on the materials used, the biofilm dislodging technique must be adapted. The US procedure was the best technic to dislodge S. epidermidis biofilm on silicone, piccline, peripheral venous catheter but not endotracheal tube. This suggested that scientists should compare themselves different methods before designing a protocol of biofilm study on a given material.
Implication of quantifying nitrate utilization and CO2 assimilation of Brassica napus plantlets in vitro under variable ammonium/nitrate ratios
Authors: Zhang Kaiyan , Wu Yanyou , Su Yue , Li Haitao 
Published: August 2022

Abstract
Background
Plantlets grown in vitro with a mixed nitrogen source utilize sucrose and CO2 as carbon sources for growth. However, it is very difficult to obtain the correct utilization proportions of nitrate, ammonium, sucrose and CO2 for plantlets. Consequently, the biological effect of ammonium/nitrate utilization, the biological effect of sucrose/CO2 utilization, and the ammonium/nitrate use efficiency for new C input derived from CO2 assimilation/sucrose utilization are still unclear for plantlets.

Results
The bidirectional stable nitrogen isotope tracer technique quantified the proportions of assimilated nitrate and ammonium in Brassica napus plantlets grown at different ammonium/nitrate ratios. The utilization proportions of sucrose and CO2 could be quantified by a two end-member isotope mixing model for Bn plantlets grown at different ammonium/nitrate ratios. Under the condition that each treatment contained 20 mM ammonium, the proportion of assimilated nitrate did not show a linear increase with increasing nitrate concentration for Bn plantlets. Moreover, the proportion of assimilated CO2 did not show a linear relationship with the nitrate concentration for Bn plantlets. Increasing the nitrate concentration contributed to promoting the assimilation of ammonium and markedly enhanced the ammonium utilization coefficient for Bn plantlets. With increasing nitrate concentration, the amount of nitrogen in leaves derived from nitrate assimilation increased gradually, while the nitrate utilization coefficient underwent no distinct change for Bn plantlets.

Conclusions
Quantifying the utilization proportions of nitrate and ammonium can reveal the energy efficiency for N assimilation in plantlets grown in mixed N sources. Quantifying the utilization proportion of CO2 contributes to evaluating the photosynthetic capacity of plantlets grown with variable ammonium/nitrate ratios. Quantifying the utilization proportions of nitrate, ammonium, sucrose and CO2 can reveal the difference in the ammonium/nitrate use efficiency for new C input derived from CO2 assimilation/sucrose utilization for plantlets grown at variable ammonium/nitrate ratios.
Procedural analgesic interventions in China: a national survey of 2198 hospitals
Authors: Wang Yafeng , Xu Feng , Zhao Shuai , Han Linlin , Huang Shiqian , Zhu Hongyu , Ding Yuanyuan , Ma Lulin , Zhao Wenjing , Zhang Tianhao , Chen Xiangdong ,   Pain Group of Chinese Society of Anesthesiology, Feng Yi , Dong Tieli , Xu Zhonghuang , Lv Yan , Hua Zhen , Liu Yanhong , Bai Yanyan , Cao Song , Chen Yajun , Du Jianhua , Fan Yinghui , Han Guang , He Nong , He Xingying , He Yongjin , Hu Yanhui , Li Yanhua , Liu Dezhao , Liu Ping , Liu Silan , Ma Danxu , Ma Minyu , Ren Fei , Shang You , Shen Xiaofeng , Song Jie , Tie Muer , Wang Chunhui , Wang Feng , Wang Haitang , Wang Huishu , Wang Tiancheng , Wang Yaping , Wu Wei , Xu Hua , Xue Zhaoxia , Yu Lingzhi , Zhan Leyun , Zhang Dong , Zhang Jinjun , Wu Duozhi , Yang Dong 
Published: August 2022

Abstract
Background
Humane treatment requires the provision of appropriate sedation and analgesia during medical diagnosis and treatment. However, limited information is available about the status of procedural analgesic interventions in Chinese hospitals. Therefore, a nationwide survey was established to identify challenges and propose potential improvement strategies.

Methods
Forty-three members of the Pain Group of Chinese Society of Anesthesiology established and reviewed the questionnaire, which included (1) general information on the hospitals, (2) the sedation/analgesia rate in gastrointestinal endoscopy, labor, flexible bronchoscopy, hysteroscopy in China, (3) staff assignments, (4) drug use for procedural analgesic interventions, and (5) difficulties in procedural analgesic interventions. The data were obtained using an online questionnaire sent to the chief anesthesiologists of Chinese hospitals above Grade II or members of the Pain Group of Chinese Society of Anesthesiology.

Results
Valid and complete questionnaires were received from 2198 (44.0%) hospitals, of which 64.5% were Grade III. The overall sedation/analgesia rates were as follows: gastroscopy (50.6%), colonoscopy (53.7%), ERCP (65.9%), induced abortion (67.5%), labor (42.3%), hysteroscopy (67.0%) and fiber bronchoscopy (52.6%). Compared with Grade II hospitals, Grade III hospitals had a higher proportion of procedural analgesic interventions services except for induced abortion. On average (median [IQR]), each anesthesiologist performed 5.7 [2.3—11.4] cases per day, with 7.3 [3.2—13.6] performed in Grade III hospitals and 3.4 [1.8—6.8] performed in Grade II hospitals (z = -7.065, p < 0.001).

Conclusions
Chinese anesthesiologists have made great efforts to achieve procedural analgesic interventions, as evidenced by the increased rate. The uneven health care provided by hospitals at different levels and in different regions and the lack of anesthesiologists are the main barriers to optimal procedural analgesic interventions.
Effects of adaptive left bundle branch–optimized cardiac resynchronization therapy: a single centre experience
Authors: Feng Xiang-Fei , Yang Ling-Chao , Zhao Yan , Yu Yi-Chi , Liu Bo , Li Yi-Gang 
Published: August 2022

AbstractBackgroundAdaptive cardiac resynchronization therapy (aCRT) is associated with improved clinical outcomes. Left bundle branch area pacing (LBBAP) has shown encouraging results as an alternative option for aCRT. A technique that can be accomplished effectively using LBBAP combined with coronary venous pacing (LOT-aCRT). We aimed to assess the feasibility and outcomes of LOT-aCRT.MethodsLOT-aCRT, capable of providing two pacing modes, LBBAP alone or LBBAP combined with LV pacing, was attempted in patients with CRT indications. Patients were divided into two groups: those with LBBAP and LV pacing (LOT-aCRT) and those with conventional biventricular pacing (BVP-aCRT).ResultsA total of 21 patients were enrolled in the study (10 in the LOT-aCRT group, 11 in the BVP-aCRT group). In the LOT-aCRT group, the QRS duration (QRSd) via BVP was narrowed from 158.0 ± 13.0 ms at baseline to 132.0 ± 4.5 ms (P = 0.019) during the procedure, and further narrowed to 123.0 ± 5.7 ms (P < 0.01) via LBBAP alone. After the procedure, when LOT-aCRT implanted and worked, QRSd was further changed to 121.0 ± 3.8 ms, but the change was not significant (P > 0.05). In the BVP-aCRT group, BVP resulted in a significant reduction in the QRSd from 176.7 ± 19.7 ms at baseline to 133.3 ± 8.2 ms (P = 0.011). However, compared with LOT-aCRT, BVP has no advantage in reducing QRSd and the difference was statistically significant (P < 0.01). During 9 months of follow-up, patients in both groups showed improvements in the LVEF and NT-proBNP levels (allP < 0.01). However, compared with BVP-aCRT, LOT-aCRT showed more significant changes in these parameters (P < 0.01).ConclusionsThe study demonstrates that LOT-aCRT is clinically feasible in patients with systolic heart failure and LBBB. LOT-aCRT was associated with significant narrowing of the QRSd and improvement in LV function.
Albumin infusion in hospitalized patients with acute heart failure: a retrospective cohort study
Authors: Wang Lei , Zhao Yun-Tao 
Published: August 2022

Abstract
Background
Heart failure is frequently associated with hypoalbuminaemia and poor prognosis. Acute heart failure (AHF) patients are commonly treated with intravenous albumin to improve osmotic pressure and haemodynamics. However, the effects of exogenous albumin supplementation on the fatality rate of AHF patients have not yet been demonstrated. Therefore, the present study strived to examine the impacts of albumin injections on the mortality rate of patients with AHF.

Methods
This retrospective cohort study evaluated the clinical outcomes of all consecutive hospitalized patients. Data were collected from medical records. The primary end-point was a composite of intubation, emergency renal replacement, or mortality in a time-to-event analysis. An inverse probability-weighted multivariable Cox model was used to compare outcomes between patients who were treated with albumin and those who were not based on the propensity score.

Results
Among the 1420 consecutive patients hospitalized in our hospital with acute decompensated heart failure between 1 January 2017 and 27 February 2021, 382 were excluded, 337 (32.5%) were administered albumin (median treatment dose of 29.0 g), and 701 (67.5%) were not. The albumin exposure varied by body mass index, age group, previous diagnoses, clinical signs and symptoms, laboratory tests, and use of other drugs in the unmatched sample. The patients receiving albumin exhibited a lower serum albumin level at baseline in contrast with those who were not treated with albumin (median, 37.3 g/L vs. 31.7 g/L, respectively). Overall, primary end-point events occurred in 357 patients (34.4%) (79 died without being intubated or during an emergency renal replacement therapy, 118 were intubated and 160 had an emergency renal replacement therapy). In the inverse probability weighted multivariable analysis based on the propensity score, albumin use was not significantly associated with the composite primary end-point (hazard ratio, 1.05; 95% confidence interval, 0.75–1.47).

Conclusion
In this observational study of AHF patients hospitalized in our hospital, the administration of albumin did not show a relationship with either a greatly reduced or aggregated risk of the composite end-point of intubation, emergency renal replacement therapy, or death. Therefore, randomized controlled trials of albumin administration are needed for patients with AHF.
Serum and salivary tissue transglutaminase IGA (tTG-IGA) level in celiac patients
Authors: Ajdani Mehran , Mortazavi Nazanin , Besharat Sima , Mohammadi Saeed , Amiriani Taghi , Sohrabi Ahmad , Norouzi Alireza , Edris Ghezeljeh 
Published: August 2022

Abstract
Background
Celiac disease (CD) is a genetically determined autoimmune disease triggered by gluten consumption. Patients with these conditions have intraepithelial lymphocytosis, crypt hyperplasia, and severe intestinal atrophy. Gluten elimination is the only way to reduce this chronic inflammation. The diagnosis of CD is usually made by analyzing anti-tTG, anti-DGP, or EMA serological tests, and it is confirmed by biopsy of the duodenum.
In people with CD, xerostomia or dry mouth is a common complication. This condition causes the salivary glands to malfunction and, in turn, may result in oral plaque and periodontal disease.
By comparing salivary and serum levels of tissue transglutaminase IgA (tTG-IgA), this study aims to suggest a non-invasive method for diagnosis of CD. Furthermore, the present study evaluates the severity of xerostomia symptoms in people with CD.

Methods
In this case–control study, participants were patients referred to the internal ward of Sayyad Shirazi hospital. The control group was selected from healthy people who attended Gorgan Dental College.
In this study, an analysis of serum was performed following consent from patients. This was followed by a salivary test, and the results of both tests were compared.
The Xerostomia Inventory questionnaire was also used to determine the severity of xerostomia. As part of this study, examination of factors such as total protein concentration of saliva, albumin concentration, amylase level, pH, sodium, calcium, potassium, phosphorus, and interleukin (6, 18, and 21) were conducted.

Results
A total of 78 people were studied (aged 15 to 68), 26 were male (33.3%) and 52 were female (66.7%). In comparisons of the serum and saliva of people with and without CD, the level of amylase was higher in the latter group. The average levels of IL-6، IL-18 ،IL-21, and salivary and serum tTG were higher in people with CD. Additionally, CD patients were more likely to develop xerostomia.

Conclusion
Study findings showed that CD can reduce certain salivary enzymes and elements, as well as increase inflammatory cytokines, salivary, and serum tTG.
The management of dry mouth should also be recommended for celiac disease patients in order to prevent its complications.
Awareness and treatment of chronic hepatitis B in Malaysia-findings from a community-based screening campaign
Authors: Lim Zhuo-zhi , Teo Jau shya , Tan Ah-Choon , Lim Teck Onn 
Published: August 2022

Abstract
Introduction
In 2016 the World Health Organization (WHO) had adopted a global strategy to eliminate Hepatitis B (HBV) by 2030 through five core interventions. One of which is the “cascade of care”, the continuum of services that persons with chronic Hepatitis B Virus (HBV) should receive as they progress from screening to diagnosis to treatment to chronic care. We determined the prevalence of the awareness and treatment of chronic HBV in Malaysia based on a large sample data from a screening campaign.

Methods
A total of 10,436 subjects participated in the HBV screening campaign organized by the Hepatitis Free Pahang Malaysia (HFP). Between in 2018 and 2019, HFP organized a total of 109 health fairs in partnership with local non-governmental organizations (NGO) to conduct HBV screening mostly in small towns and villages largely in the state of Pahang. All screen-positive subjects were recalled to undergo laboratory-based HBsAg and HBV DNA tests. Patients with confirmed chronic HBV were referred to local health services, while continued being monitored by HFP.

Results
We estimated 13.1% of Malaysian adults aged 20 or older with chronic HBV were aware of their HBV status, and of those only 0.7% had received prior anti-viral treatment, but among those with baseline HBV DNA level > 20,000 IU/ml, 15.6% were subsequently treated. Tenofovir disoproxil fumarate was the only medicine used on all treated patients.

Conclusion
Few Malaysian adults with HBV were aware of their infection and even less received anti-viral therapy. Concerted public health efforts are urgently needed to improve HBV screening and care cascade in order to meet WHO’s targets for HBV elimination.
Significance of levothyroxine treatment on serum lipid in pregnant women with subclinical hypothyroidism
Authors: Yang Yuxi , Yuan Huabing , Wang Xueran , Zhang Zheng , Liu Ruixia , Yin Chenghong 
Published: August 2022

Abstract
Background
There is no consensus reference range for serum lipid levels during pregnancy. The benefit of levothyroxine (L-T4) on serum lipid levels are unclear among pregnant women with subclinical hypothyroidism (SCH).

Objective
To determine the recommended reference ranges for serum lipid concentrations during pregnancy and effects of L-T4 treatment on serum lipids in pregnant women with SCH.

Design
Cohort study.

Methods
A analysis of 20,365 women in the first trimester was conducted at Beijing Obstetrics and Gynecology Hospital, Capital Medical University during 2018–2020. After excluding women with adverse pregnancy outcomes, we determined the reference range of serum lipid in the first and third trimesters of pregnancy by using median and quartile to determine appropriate percentiles. Next, we divided into three groups as follows: SCH L-T4 treatment group (n = 319), SCH non-intervention group (n = 103) and the control group(n = 9598).

Results
The recommended reference range for serum lipids in the first trimester of pregnancy should be: TC < 5.33 mmol/L, TG < 1.73 mmol/L, LDL-C < 3.12 mmol/L and HDL-C > 1.1 mmol/L, and in third trimester of pregnancy should be: TC < 8.47 mmol/L, TG < 4.86 mmol/L, LDL-C < 5.3 mmol/L and HDL-C > 1.34 mmol/L.
There are significant differences in TC and LDL-C levels between SCH treatment group and SCH non-intervention Group (P = 0.043, P = 0.046; respectively).

Conclusions
We determine the recommended reference ranges for serum lipid concentrations during pregnancy. TC and LDL-C levels in pregnant women with SCH could improve after L-T4 treatment.
Poor treatment responses were related to poor outcomes in pediatric B cell acute lymphoblastic leukemia with KMT2A rearrangements
Authors: Wen Jinquan , Zhou Min , Shen Yali , long Yueting , Guo Yuxia , Song Lin , Xiao Jianwen 
Published: August 2022

Abstract
Background
The KMT2A gene, formerly named the MLL gene, is rearranged (KMT2Ar) in 70–75% of infants, 5–6% of children and 10–15% of adult patients with B cell acute lymphoblastic leukemia (B-ALL). The outcome after chemotherapy of pediatric cases remains poor, and only a few studies have investigated the clinical and laboratory features, treatment response and prognosis in Chinese populations.

Methods
A total of 48 B-ALL children with KMT2Ar were enrolled in the study, and clinical and laboratory data were collected and analyzed by age group. The relationship between prognosis and traditional risk factors and treatment response was investigated for these patients who received chemotherapy.

Results
The 48 enrolled patients included 28 males and 20 females; 18 (37.50%) or 30 (62.50%) patients were an age of < 12 m (infant B-ALL) or of > 12 m at onset. An initial WBC count of 300 × 109/L was detected in 7 (14.58%) patients; testicular leukemia (TL) or central nervous system involvement was found in 5 (10.41%) or 3 (6.25%) patients, respectively. Statistical differences were not found in the age groups of sex or initial WBC count, whereas TL was more common in the infant group (P < 0.05). 11q23 was detected in 18 patients; KMT2Ar was detected in 46 (95.83%) or 45 (93.75%) patients by FISH or multiplex RT–PCR technology, respectively; RNA-seq data were obtained for 18 patients, and 3 patients with uncommon KMT2Ar were identified. KMT2A-AFF1, KMT2A-MLLT3 and KMT2A-MLLT1 were the most common transcripts. Statistical differences were not found in treatment response by age groups, including dexamethasone induction, bone marrow (BM) smear status and minimal residual disease (MRD) level at different time points (TP), treatment-related mortality (TRM), or complete remission (CR) rate (P > 0.05); MRD levels monitored by FCM or PCR were unequal at the same TP. Four patients died of treatment, and TRM was 8.33%; 40 patients achieved CR, and the CR rate for the cohort was 83.33%. Seven patients quit, 15 patients relapsed, and the 5 yr cumulative relapse rate was 59.16 ± 9.16%; the 5 yr prospective EFS (pEFS) for patients who were included or excluded from the TRM group was 36.86 ± 8.48% or 40.84 ± 9.16%, respectively. Multivariate analysis for prognosis and hazard ratio was performed for 37 patients without TRM and revealed that an initial WBC count of > 300 × 109/L and a positive level of FCM-MRD were strongly related to a poor outcome for B-ALL patients with KMT2Ar (P < 0.05).