bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiple Traditional Chinese Medicine interventions for idiopathic pulmonary fibrosis
Authors: Zhang Hao-Yang , Pang Li-Jian , Lv Xiao-Dong , Liu Chuang , Nan Ming-Hua
Published: September 2020

Background:

The therapeutic strategies of idiopathic pulmonary fibrosis (IPF) tend to be comprehensive. Improving the major symptoms and quality of life (QoL) is as important as postponing the process of fibrosis. However, only pirfenidone and nintedanib conditionally recommended by guidelines and no definite proof indicate that they can significantly ameliorate the main symptoms and QoL of IPF sufferers. At present, multiple types of Traditional Chinese Medicine (TCM) interventions alone or in combination with conventional western medicine managements are widespreadly applied in IPF treatment, which seemingly have a promising clinical effect, especially in ameliorating the main symptoms and improving QoL. Subsequently, the number of relevant studies in systematic reviews(SRs) and meta-analyses of randomized controlled trials(RCTs) increased significantly. Hence, we plan to implement an overview to collect, evaluate, and summarize the results of these SRs.

Methods:

An all-round literature retrieval will be conducted in 9 electronic databases, including PubMed, EMBASE, CINAHL, Cochrane Library, Epistemonikos, CNKI, CBM, Wanfang, and VIP. We will focus on the systematic review and meta-analysis of RCTs for multiple TCM interventions alone or in combination with routine western medicine measures in IPF treatment. The main outcomes we follow with interest include the improvement of major symptoms (cough, dyspnea) and QoL. Secondary outcomes will consist of minor symptoms improvement, clinical total effective rate, lung function, blood gas analysis, 6-minute walk text, adverse events, acute exacerbation, all-cause mortality, and IPF-related mortality. Two reviewers will independently select the SRs satisfactory with the enrolling criteria, extract key characteristics, and datas on predefined form, evaluate methodological quality by AMSTAR-2, ROBIS and PRISMA tools, and the quality of evidences adopting GRADE method. In case of any divergence will be reached an agreement by discussion or adjudicated by a third senior reviewer. We will perform a narrative synthesis of the proofs from SRs included.

Results:

The findings of this overvew will be presented at relevant conferences and submitted for peer-review publication.

Conclusions:

We expect to obtain comprehensive and reliable evidence of IPF treated by diversified TCM interventions from the potential standard SRs, which may provide suggestions for future RCTs and SRs.

Registration number:

INPLASY 202080110
The clinical efficacy of traditional Chinese medicine in the treatment of malignant pleural effusion
Authors: Lin Zhen , Jiang Mengyuan , Gao Lirong , Zhang Huachun
Published: September 2020

Background:

The objective of this meta-analysis was to summarize and identify the available evidence from studies to estimate the clinical value of traditional Chinese medicine (TCM) in the treatment of malignant pleural effusion (MPE). And provides clinicians with evidence on which to base their clinical decision making.

Methods:

This review will include all studies comparing clinical efficacy of TCM in the treatment of MPE. The search strategy will be performed in 9 databases. We will not establish any limitations to language and publication status, published from inception to the July, 2020. Two reviewers will screen, select studies, extract data, and assess quality independently. Outcome is clinical efficacy, QLQ-C30 questionnaire and safety. The methodological quality including the risk of bias of the included studies will be evaluated. We will carry out statistical analysis using RevMan 5.3 software.

Results:

This study will summarize current evidence to assess the efficacy and safety of TCM in the treatment of MPE.

Conclusion:

The findings of this study will provide helpful evidence for the clinician, and will promote further studies, as well as studying the value of TCM.
The acute and chronic effects of high-intensity exercise in hypoxia on blood pressure and post-exercise hypotension
Authors: Kleinnibbelink Geert , Stens Niels A. , Fornasiero Alessandro , Speretta Guilherme F. , Van Dijk Arie P.J. , Low David A. , Oxborough David L. , Thijssen Dick H.J.
Published: September 2020

Background:

Acute exercise leads to an immediate drop in blood pressure (BP), also called post-exercise hypotension (PEH). Exercise in hypoxia is related to additional vasodilation, potentially contributing to more profound PEH. Therefore, we investigated the impact of hypoxia versus normoxia on the magnitude of PEH. Second, we examined whether these changes in PEH relate to the BP-lowering effects of 12-week exercise training under hypoxia.

Methods:

In this prospective study, 21 healthy individuals (age 22.2 ± 3.0 years, 14 male) performed a 45-minute high-intensity running exercise on 2 different days in a random order, under hypoxia (fraction of inspired oxygen 14.5%) and normoxia (fraction of inspired oxygen 20.9%). BP was examined pre-exercise (t = 0) and at t = 15, t = 30, t = 45, and t = 60 minutes post-exercise. Afterward, subjects took part in a 12-week hypoxic running exercise training program. Resting BP was measured before and after the 12-week training program.

Results:

Acute exercise induced a significant decrease in systolic BP (systolic blood pressure [SBP], P = .001), but not in diastolic BP (diastolic blood pressure [DBP], P = .113). No significant differences were observed in post-exercise BP between hypoxic and normoxic conditions (SBP, P = .324 and DBP, P = .204). Post-exercise changes in SBP, DBP, and mean arterial pressure significantly correlated to the 12-week exercise training-induced changes in SBP (r = 0.557, P = .001), DBP (r = 0.615, P < .001), and mean arterial pressure (r = 0.458, P = .011).

Conclusion:

Our findings show that hypoxia does not alter the magnitude of PEH in healthy individuals, whilst PEH relates to the BP-lowering effects of exercise. These data highlight the strong link between acute and chronic changes in BP.
Admitted AIDS-associated Kaposi sarcoma patients
Authors: Vally Faheema , Selvaraj Wencilaus Margret Pious , Ngalamika Owen
Published: September 2020

Kaposi sarcoma (KS) is an AIDS-defining angioproliferative malignancy associated with high morbidity and mortality. Most KS patients in regions with high incidence such as sub-Saharan Africa present late with advanced stage disease. Admitted KS patients have high mortality rates. Factors associated with mortality of admitted KS patients are poorly defined.

We conducted a retrospective file review to ascertain reasons for admission and identify factors associated with mortality of admitted HIV-associated (epidemic) KS patients in Zambia. Baseline study variables were collected, and patients were retrospectively followed from admission to time of discharge or death.

Mortality rate for admitted epidemic KS patients was high at 20%. The most common reasons for admission included advanced KS disease, severe anemia, respiratory tract infections, and sepsis. The majority (48%) of admitted patients had advanced clinical stage with visceral involvement on admission. Clinical predictors of mortality on univariate analysis included visceral KS [odds ratio (OR) = 13.74; 95% confidence interval (95% CI) = 1.68–113; P = 0.02), fever (OR = 26; 95% CI = 4.85–139; P = .001), and sepsis (OR = 35.56; 95% CI = 6.05–209; P = .001). Baseline hemoglobin levels (5.6 vs 8.2 g/dL; P = .001) and baseline platelet counts (63 x 10^9/L vs 205 x 10^9/L; P = .01) were significantly lower in mortalities vs discharges. Baseline white cell counts were higher in mortalities vs discharges (13.78 x 10^9/L vs 5.58 x 10^9/L; P = .01), and HIV-1 viral loads at the time of admission were higher in mortalities vs discharges (47,607 vs 40 copies/μL; P = .02). However, only sepsis (or signs and symptoms of sepsis) were independently associated with mortality after controlling for confounders.

In conclusion, common reasons for admission of epidemic KS patients include advanced disease, severe anemia, respiratory tract infections, and signs and symptoms of sepsis. Signs and symptoms of sepsis are independent predictors of mortality in these patients.
Enhanced immune reaction resulting from co-vaccination of WT1 helper peptide assessed on PET-CT
Authors: Nakata Jun , Isohashi Kayako , Morimoto Soyoko , Itou Ryota , Kamiya Takashi , Matsuura Ai , Nakajima Hiroko , Fujiki Fumihiro , Nishida Sumiyuki , Hasii Yoshiko , Hasegawa Kana , Nakatsuka Shinichi , Hosen Naoki , Tsuboi Akihiro , Oka Yoshihiro , Kumanogoh Atsushi , Shibano Masaru , Munakata Satoru , Oji Yusuke , Hatazawa Jun , Sugiyama Haruo
Published: September 2020

It has become evident that positron emission tomography/computed tomography (PET-CT) using 2-deoxy-2-[F-18]fluoro-D-glucose (FDG) (FDG PET-CT) can detect anti-tumor immune response induced by various immunotherapies. To evaluate whether FDG PET-CT could detect anti-cancer immune response caused by cancer vaccine therapy, we performed a retrospective analysis of FDG PET-CT imaging of patients who were treated with Wilms Tumor 1 (WT1) vaccine therapy in Osaka University during July 2008 and June 2018. Increased FDG uptakes were detected in WT1-vaccinated skin and their draining lymph nodes during the repeated vaccination. While the FDG uptakes seemed to decrease with time after the cessation of WT1 peptide vaccinations, persistence of FDG uptakes for years in WT1-vaccinated skin were also observed in 2 cases who showed good clinical course. Moreover, the FDG uptakes of patients treated with the combination vaccine of WT1 specific cytotoxic T cell (CTL) and helper peptides were significantly stronger than of those treated with the WT1 CTL peptide alone. Since it is evident that the combination vaccine can induce a more robust anti-tumor immunity than can CTL peptide vaccine alone, the FDG uptakes in WT1-vaccinated skin might reflect the degree of immune response. These results suggest that PET-CT might be a good tool for prediction of anti-tumor immune response induced by WT1 vaccine therapy. Larger scale prospective studies therefore seem to be warranted.
Clinical significance and influencing factors of fibrinogen in ANCA-associated vasculitis
Authors: Zhang Naidan , Sun Jiaxiang , Ji Chaixia , Zhou Yusha , Bao Xiao , Yuan Chengliang
Published: September 2020

Hypercoagulable is an important pathological state in anti-neutrophil cytoplasmic antibody-associated vasculitis (AAV). Fibrinogen (FIB) is the main protein in coagulation process. In this study, we aimed to investigate the clinical significance and influencing factors of FIB in AAV from Southwest China.

A retrospective study was performed on AAV patients from Peoples Hospital of Deyang City from January 2007 to December 2018. Demographic and clinical characteristics were collected.

A total of 463 AAV patients were included. In Wilcoxon rank sum test, FIB was significantly higher in AAV active group than inactive group (P = .005). FIB was also higher in bacterial infection group than in non-infection group both in active group (P = .008) and inactive group (P = .017). In receiver operating characteristic (ROC) curve analysis, the critical value of FIB for diagnosis of bacterial infection between AAV active and inactive groups was 3.385 g/L (P = .030), with sensitivity of 70.2% and specificity of 52.9%. In the multivariate analysis of variance (MANOVA), estimated glomerular filtration rate (eGFR) was shown to be an independent factor for FIB (P = .001). Least-significant difference showed the concentration of FIB (P < .05) increased with renal impairment, especially in endstage kidney disease (ESKD).

FIB identified a certain reference value in distinguishing AAV activity from bacterial infection. ESKD had a statistical effect on it. Influencing factors of FIB should be evaluated based on the renal function impairment of patients.
Risk of primary liver cancer associated with gallstones and cholecystectomy
Authors: Liu Tong , Siyin Sarah Tan , Yao Nan , Xu Guoshuai , Chen Yi-Tsun , Duan Ning , Li Wenqiang , Qu Jun , Liu Siqing
Published: September 2020

Previous research has revealed a positive relationship between GSD, cholecystectomy and primary liver cancer (PLC). However, previous studies had several limitations including the retrospective design, narrow assessment of potential confounders and lack of competing risk models in time-to-event analyses. We conducted a large prospective cohort study to explore the relationship between GSD, cholecystectomy and PLC. A total of 95,021 participants who had not been diagnosed with PLC previously were enrolled from the Kailuan Cohort study. Demographic characteristics and biochemical parameters were recorded at baseline for all participants. We used Cox regression models and competing risk regression models to evaluate the association of GSD and cholecystectomy with the risk PLC. A total of 306 incidental PLC cases were identified during a median follow-up of 9.05 (8.75–9.22) years per participant. Compared with the normal group, the multivariable HRs (95%CI) for the association of GSD and cholecystectomy with PLC were 1.77 (1.05–2.94), 5.25 (1.95–14.17). In the CS model, the multivariable HRs (95%CI) was 1.76 (1.05–2.94) for the association of GSD and cholecystectomy with PLC and 5.25 (1.95–14.17) for GSD and cholecystectomy. Similar results were also obtained in the SD model with corresponding multivariate HRs (95%CI) of 1.75 (1.01–3.00), 5.22 (1.90–14.07) in the GSD group and cholecystectomy group, respectively. GSD and cholecystectomy were associated with an elevated risk of PLC.

Registration number: ChiCTR–TNRC–11001489.
Higher hypertension prevalence, lower incidence, and aggressive treatment with decreasing mortality, cardiovascular, and cerebrovascular incidence in Taiwan from 2005 to 2010
Authors: Liao Chia-Te , Wu Pei-Chih , Shih Jung-Chang , Cheng Tain-Junn , Wu Wen-Shiann
Published: September 2020

Hypertension continues to be an important public health concern because of its associated morbidity, mortality, and economic impact on society. The aims of this study are to compare the secular changes in age-stratified hypertension prevalence, incidence, co-morbidity, and 3 years of cardiovascular outcome in Taiwan in the years 2005 and 2010.

We enrolled hypertensive individuals from the datasets of the Longitudinal Health Insurance Database (LHID) in 2005 and 2010 in Taiwan separately. We analyzed the hypertension prevalence, incidence, medication treatment, and associated morbidities. The risks of cardiovascular and cerebrovascular events and all-causes mortalities among the hypertensive individuals were evaluated in 3 years of follow-up.

There was an increased prevalence of hypertension but decreased incidence of hypertension in those over 65 from 2005 to 2010. Dyslipidemia was the highest rate of co-morbidity in 2005 and 2010. The most frequent categories of anti-hypertensive agents prescribed was 1 or 2 for both 2005 and 2010. Calcium channel blockers were the most common anti-hypertensive agents prescribed, followed by Angiotensin converting enzyme inhibitors/Angiotensin receptor blockers. After 3 years of follow-up, the risks of coronary artery disease (CAD), cerebrovascular diseases (CVD) as well as death were less in 2010 than in 2005 in Taiwan.

Our study showed that hypertension individuals had an increased prevalence, younger age, decreased incidence, increased medication treatment associated with decreased the CAD, CVD, and mortalities in 2010 compared to 2005 in Taiwan.
Efficacy and safety of Chinese herbal compound in the treatment of functional constipation
Authors: Ji Lijiang , Fan Yihua , Li Linhui , Bai Huiwen , Weng Liping , Zhao Ping
Published: September 2020

Background:

Functional constipation refers to constipation without organic lesions caused by dietary factors, mood depression, changes in life rules, and poor bowel habits. Clinically, constipation is mainly manifested by changes of stool texture, difficulty or lack of bowel movement, and dry stool. Sometimes, it can be accompanied by abdominal distension and abdominal discomfort. Chinese herbal compound is a prescription which is composed of 2 or more medicinal flavors and is designed for relatively certain diseases and syndromes. Clinical studies have shown that TCM compounds have a good therapeutic effect on functional constipation, but there is no evidence of evidence-based medicine. The purpose of this study is to systematically evaluate the efficacy and safety of TCM compounds in the treatment of functional constipation, and to provide evidence-based basis for the clinical application of TCM compounds in the treatment of constipation.

Methods:

A systematic search was performed on English database (PubMed, Embase, Web of Science, the Cochrane Library) and Chinese database (CNKI, Wanfang, Weipu (VIP), CBM), in addition to the manual retrieval of Baidu and Google academic for randomized controlled trials (RCTs) on the treatment of functional constipation with Chinese herbal compound. The retrieval time limit was from the establishment of the database to August 2020. Two researchers independently screened the literature, extracted the data and evaluated the quality of the included studies. A meta-analysis was performed using RevMan5.3 software.

Results:

In this study, the efficacy and safety of TCM herbal compounds in the treatment of functional constipation were evaluated by the overall effective rate, recovery rate, colonic transmission function, and other indicators.

Conclusions:

This study will provide reliable evidence-based evidence for the clinical application of Chinese herbal compound in the treatment of functional constipation.

OSF Registration number:

DOI 10.17605/OSF.IO/D5ECF.
Imaging features of periostitis as a manifestation of IgA vasculitis
Authors: Noh Ji Hoon , Chung Bo Mi , Kim Wan Tae
Published: September 2020

Introduction:

Periostitis in systemic vasculitis is very rare with only a few previously reported cases. The reported cases were seen in polyarteritis nodosa or Takayasu arteritis. We report the first case of periostitis associated with IgA vasculitis with demonstration of computed tomography (CT), magnetic resonance imaging (MRI) features, and serial changes of radiographs.

Patient concerns:

A 74-year-old man visited an orthopedic outpatient clinic for pain in both lower legs and left ankle pain. He underwent a total ankle arthroplasty of the left ankle 3 years ago. His medical history disclosed IgA vasculitis/nephropathy caused by cephalosporin antibiotic class 5 months earlier. Plain radiography, MRI of the right lower leg, CT scan of the left ankle showed single lamellar to spiculated periosteal reactions at both tibia, fibula and left calcaneus. There was no evidence of bone or soft tissue mass lesions or cortical destruction.

Diagnosis:

We concluded that this was a case of periosteal reactions associated with IgA vasculitis for the following reasons: (1) periosteal biopsy was negative for tumor. (2) there was no pulmonary lesion on chest radiography and CT, no history of trauma, inflammatory arthritis, metabolic disease, or genetic disease that could cause periostitis at multiple bones, (3) the initial MRI showed predominant signal changes around the tibial and fibular shafts, possibly explaining subsequent periosteal reactions, and (4) symptoms subsided with conservative treatment and follow-up radiographs showed remodeling of periosteal reactions.

Interventions:

The patient took conservative management.

Outcomes:

His calf pain improved, and a radiograph 7 months later showed remodeling to the solid or single lamellar periosteal reaction along the both tibia and left fibula.

Conclusion:

Awareness of this uncommon manifestation would help differential diagnosis of periostitis and could help decrease the patient's anxiety. It should also be noted that periosteal reactions by benign entities could cause aggressive-looking periosteal reactions in post-operative regions.
Complementing Root Cause Analysis With Improvement Strategies to Optimize Venous Thromboembolism Prophylaxis in Patients With Epidural Catheters
Authors: Slade Justin J. , Wrzesniewski Carolyn E. , Hunter Oluwatobi O. , Allaudeen Nazima
Published: September 2020

Background and Objectives:

High reliability organizations in health care must identify defects and systematically approach causal factors with subsequent process redesign to achieve goals important to patients, families, and staff. Root cause analysis (RCA) is a commonly leveraged strategy for reviewing adverse events and can yield immense benefits toward patient safety when applied alongside complementary change management strategies such as Lean and Six Sigma. We performed an RCA in response to a hospital-acquired venous thromboembolism (VTE) event in a postoperative patient for which pharmacologic VTE prophylaxis was not appropriately resumed following removal of an epidural catheter.

Methods:

A multidisciplinary stakeholder team was assembled to further understand the details of the event. A current process map was created and non-value-added steps were identified. Causal analysis revealed that frequent staff turnover, variable methods of communication between stakeholders, inconsistent responsibilities with respect to ordering and administering pharmacologic VTE prophylaxis, and lack of an established standard work process were key contributors toward the defect of concern. Several countermeasures were introduced to combat these identified root causes, including shifting responsibility for managing VTE prophylaxis orders periepidural catheter removal from the surgical house staff to our regional anesthesia service, and creation of an epidural catheter heparin restart order set, which in one step places an order to resume prophylaxis following catheter removal at a specific time. Recommendations from this session were disseminated to staff through previously established huddles that are a component of our daily management system.

Results:

Postintervention, review of our updated process demonstrated a reduction in variability through establishment of standard work that is primarily owned by a constant factor in this care pathway (our regional anesthesia team). On review of the subsequent 10 cases of patients with epidural catheters, all patients receiving pharmacologic VTE prophylaxis had a maximum of 1 dose stopped for epidural catheter removal, therefore minimizing time without VTE prophylaxis.

Conclusions:

RCA can be utilized in the aftermath of an adverse event to establish causal factors and identify countermeasures to prevent recurrence of such an event. It can be further augmented with additional change management strategies including Lean, Six Sigma, the Model for Improvement, and failure modes and effects analysis. These strategies allowed us to design effective error-reducing strategies to achieve a more reliable process, which yielded reduced VTE prophylaxis administration defects that in turn has prevented recurrence of hospital-acquired VTE in patients with epidural catheters.
Effects of rice varieties (Oryza sativa L.) on the
quality of sponge cake
Authors: Jung Hee Nam
Published: September 2020

This study aimed to compare the physicochemical properties of four rice varieties
(‘Suwon 541’, ‘Suwon 542’, ‘Ilmi’,
‘Goami’) and their effect on the quality of sponge cake. The
amylose contents in ‘Suwon 541’, ‘Suwon 542’,
‘Ilmi’, and ‘Goami’ were 19.69%,
18.15%, 18.62%, and 26.92%, respectively. The average
particle size of ‘Suwon 542’ (21.87 μm) was significantly
lower than that of the other varieties. The water absorption index (WAI) was
highest for ‘Goami’ and the water solubility index (WSI) was
highest for ‘Suwon 541’. The amylogram results indicated that
initial pasting temperature was the highest for ‘Suwon 541’, where
as the setback was the highest for ‘Goami’ and the lowest for
‘Ilmi’. ‘Suwon 541’ flour exhibited low volume and
high cake hardness because of its high initial pasting temperature. Sponge cakes
prepared with ‘Suwon 542’, which exhibited fine grain size and low
WAI and WSI, had low hardness owing the low specific gravity of the batter and
high cake volume. The low-setback ‘Ilmi’ flour was expected to
have a retarding retrogradation effect on cakes. Sponge cakes prepared with
‘Goami’ flour possessed good characteristics although its high
setback was expected to degrade the texture due to rapid retrogradation. The
overall acceptability was the highest for ‘Suwon 542’ and
‘Ilmi’. Thus, ‘Suwon 542’ and ‘Ilmi’
were found to have a more positive effect on the quality of sponge cakes
compared with the other varieties.
Determination of optimum processing conditions for extruded rice cake
using response surface methodology
Authors: Kim Hyung Joo , Yoon Won Byong
Published: September 2020

The optimum processing conditions for extruded rice cakes were determined using
response surface methodology. Lab-scale processing equipment was developed and
tested under various processing conditions. This study specifically attempted to
determine the ideal condtions for producing rice cakes by applying different
extrusion conditions, namely, different moisture contents, rice flour particle
size, steaming time, and number of extrusions. The quality properties of the
rice cakes were evaluated by measuring their texture properties and color
values. The response surface method was applied to design the experiment and to
develop model equations based on the experimental data. The target quality
values were determined by measuring the quality parameters of commercial rice
cakes. The samples were prepared with different ratios of water content in the
label and with different types of rice flour (well-milled and dried rice flour)
to extend the feasibility. For samples prepared with dried rice flour using a
batch:water content of 1:0.4, the optimum steaming time and number of extrusions
were determined to be approximately 116 min and one, respectively, whereas they
were 115 min and one, respectively, for the sample with the ratio 1:0.5. The
optimum texture properties for the sample produced with flour prepared at the
lab scale were achieved using 111 min of steaming and three extrusion cycles.
Thus, the optimum processing conditions for producing extruded rice cakes using
lab-scale production units were determined.
Evaluation of microbial contamination levels and biogenic amines
content in over-ripened kimchi
Authors: Lim Eun-Seo
Published: September 2020

The purpose of this study was to determine the microbial contamination and the
content of biogenic amines (BA) in over-ripened kimchi prepared with different
kinds of salted and fermented seafoods during fermentation. The number of
bacterial cells in the overall kimchi samples reached a maximum after 3–6 months
of fermentation and then gradually decreased thereafter. Yeasts were detected
from the overall kimchi samples after 3 months of fermentation, however the
amounts of yeast cells were significantly lower than lactic acid bacteria (LAB)
cells throughout the fermentation periods. As the fermentation progresses, pH
levels and salinity of all kimchi samples gradually decreased, whereas
titratable acidity values and amino-type nitrogen and volatile base nitrogen
contents sharply increased. There were significant differences (p<0.05)
in the microbiological and physicochemical properties observed in freshly-made
kimchi and over-ripened kimchi prepared by using different kinds of salted and
fermented seafoods. Immediately after preparation, BA-producing LAB were
isolated from kimchi samples with salted and fermented seafoods, and the strain
numbers of the bacteria in over-ripened kimchi were significantly higher than in
freshly-made kimchi. In contrast, the reduction of histamine and putrescine
contents in some over-ripened fermented kimchi samples prepared with
‘Kanari-aekjeot’ and ‘Myeolchi-aekjeot’ was observed
during the late stage of fermentation, which may be the effect of microorganisms
with antibacterial activity against BA-producing bacteria or BA-degrading
bacteria.
Risk factors for mortality among hospitalized patients with COVID-19
Authors: Incerti Devin , Rizzo Shemra , Li Xiao , Lindsay Lisa , Yau Vince , Keebler Dan , Chia Jenny , Tsai Larry
Published: September 2020

Objectives

To develop a prognostic model to identify and quantify risk factors for mortality among patients admitted to the hospital with COVID-19.

Design

Retrospective cohort study. Patients were randomly assigned to either training (80%) or test (20%) sets. The training set was used to fit a multivariable logistic regression. Predictors were ranked using variable importance metrics. Models were assessed by C-indices, Brier scores, and calibration plots in the test set.

Setting

Optum® de-identified COVID-19 Electronic Health Record dataset.

Participants

17,086 patients hospitalized with COVID-19 between February 20, 2020 and June 5, 2020.

Main outcome measure

All-cause mortality during hospital stay.

Results

The full model that included information on demographics, comorbidities, laboratory results and vital signs had good discrimination (C-index = 0.87) and was well calibrated, with some overpredictions for the most at-risk patients. Results were generally similar on the training and test sets, suggesting that there was little overfitting.

Age was the most important risk factor. The performance of models that included all demographics and comorbidities (C-index = 0.79) was only slightly better than a model that only included age (C-index = 0.76). Across the study period, predicted mortality was 1.2% for 18-year olds, 8.4% for 55-year olds, and 28.6% for 85-year olds. Predicted mortality across all ages declined over the study period from 21.7% by March to 13.3% by May.

Conclusion

Age was the most important predictor of all-cause mortality although vital signs and laboratory results added considerable prognostic information with oxygen saturation, temperature, respiratory rate, lactate dehydrogenase, and white blood cell count being among the most important predictors. Demographic and comorbidity factors did not improve model performance appreciably. The model had good discrimination and was reasonably well calibrated, suggesting that it may be useful for assessment of prognosis.
Instrumented individuals are not representative of the population. Survival of wolverines with and without GPS collars
Authors: Milleret Cyril , Bischof Richard , Dupont Pierre , Brøseth Henrik , Odden John , Mattisson Jenny
Published: September 2020

Results from biologging studies are often scaled up to population-level inferences and this begs the question: Are instrumented animals representative of the population given the potential bias in individual selectivity, the influence of capture, handling and wearing bio-loggers? The answer is elusive due to the challenges of obtaining comparable data from individuals without bio-loggers. Using non-invasive genetic data of a large carnivore, the wolverine (Gulo gulo) in Scandinavia, and an open-population spatial capture-recapture model, we were able to estimate and compare survival rates of individuals fitted with GPS collars versus individuals that had never been captured and collared. We found that mortality of GPS collared individuals was 47% lower compared to individuals without GPS collars. While instrumented and non-instrumented wolverines had similar risks of dying from legal culling, GPS collared individuals displayed lower mortality rates due to causes other than legal culling. Reports of positive effects of biologging on the fitness of individuals are rather uncommon and we argue that the most likely explanation is that GPS-collars could shield animals from poaching. Our results highlight the challenges of drawing population level inferences for large carnivores when using data from an instrumented sample of the population.
Habitat differences filter functional diversity of low dispersive microscopic animals
Authors: Martínez Alejandro , García-Gómez Guillermo , García-Herrero Álvaro , Sánchez Nuria , Pardos Fernando , Izquierdo-Muñoz Andrés , Fontaneto Diego , Mammola Stefano
Published: September 2020

Whereas the study of patterns of distribution of microscopic animals has long been dominated by the ubiquity paradigm, we are starting to appreciate that microscopic animals are not as widespread as previously thought and that habitat preferences may have a strong role in structuring their patterns of occurrence. However, we still ignore to what extent and through which mechanisms the environment selects for specific communities or traits in microscopic animals. This gap is partly due to the lack of data on the relevant traits of many species, and partly because measuring environmental variables at an appropriate resolution may be problematic.

We here overcome both issues by analysing the functional space of marine mite communities living in a sea-grass (Posidonia oceanica) meadow across two habitats: the leaves and the matte. The strictly benthic lifestyle and the conserved morphology of mites allow for unambiguous characterization of their functional traits, while the discrete nature of the two habitats alleviates the uncertainty in their ecological characterization.

Our results show that habitat filters the distribution of certain traits favouring a higher diversity, dispersion, and evenness of functional traits in the matte than in the leaves. We further observed temporal variations in the functional diversity of communities, potentially following the seasonal renovation and decay of seagrass leaves. However, in spite of the stark ecological differences between the two habitats and across seasons, the filtering effect is partial and affects mostly relative species abundances.

We conclude that in other microscopic organisms, habitat filtering might appear even more subtle especially if they are capable of long distance dispersal or occur in ecological systems where environmental variables vary continuously or fluctuate through time. Our study therefore emphasises the need of moving from a merely taxonomical toward a functional view of ecological studies of microscopic organisms if we want to achieve a mechanistic understanding of their habitat and distribution patterns.

Data availability statement

Raw data and R script to generate the analyses will be deposited in a public repository upon acceptance.
Two Regulators of G-protein signaling (RGS) proteins FlbA1 and FlbA2 differentially regulate fumonisin B1 biosynthesis in Fusarium verticillioides
Authors: Yan Huijuan , Zhou Zehua , Shim Won Bo
Published: September 2020

Fumonisins are a group of mycotoxins produced by maize pathogen Fusarium verticillioides that pose health concerns to humans and animals. Yet we still lack a clear understanding of the mechanism of fumonisins regulation during pathogenesis. The heterotrimeric G protein complex, which consists of Gα, Gβ, and Gγ subunits, plays an important role in transducing signals under environmental stress. Furthermore, regulators of G-protein signaling (RGS) proteins act as negative regulators in heterotrimeric G protein signaling. Earlier studies demonstrated that Gα and Gβ subunits are positive regulators of fumonisin B1 (FB1) biosynthesis and that two RGS genes, FvFlbA1 and FvFlbA2, were highly upregulated in Gβ deletion mutant ΔFvgbb1. Saccharomyces cerevisiae and Aspergillus nidulans contain a single copy of FlbA, but F. verticillioides has two putative FvFlbA paralogs, FvFlbA1 and FvFlbA2. Importantly, FvFlbA2 has a negative role in FB1 regulation. In this study, we further characterized functional roles of FvFlbA1 and FvFlbA2. While ΔFvflbA1 deletion mutant exhibited no significant defects, ΔFvflbA2 and ΔFvflbA2/A1 mutants showed thinner aerial hyphal growth while promoting FB1 production. FvFlbA2 is required for proper expression of key conidia regulation genes, including putative FvBRLA, FvWETA, and FvABAA, while suppressing FUM21, FUM1, and FUM8 expression. Split luciferase assays suggest that FvFlbA paralogs interact with key heterotrimeric G protein components to impact F. verticillioides FB1 production and asexual development.
Comparative Effectiveness of Famotidine in Hospitalized COVID-19 Patients
Authors: Shoaibi Azza , Fortin Stephen , Weinstein Rachel , Berlin Jesse A. , Ryan Patrick
Published: September 2020

Background

Famotidine has been posited as a potential treatment for COVID-19. We compared the incidence of COVID-19 outcomes (i.e., death; and death or intensive services use) among hospitalized famotidine users vs. proton pump inhibitors (PPIs) users, hydroxychloroquine users or famotidine non-users separately.

Methods

We constructed a retrospective cohort study using data from COVID-19 Premier Hospital electronic health records. Study population were COVID-19 hospitalized patients aged 18 years or older. Famotidine, PPI and hydroxychloroquine exposure groups were defined as patients dispensed any medication containing one of the three drugs on the day of admission. The famotidine non-user group was derived from the same source population with no history of exposure to any drug with famotidine as an active ingredient prior to or on the day of admission. Time-at-risk was defined based on the intention-to-treat principle starting 1 day after admission to 30 days after admission. For each study comparison group, we fit a propensity score (PS) model through large-scale regularized B logistic regression. The outcome was modeled using a survival model.

Results

We identified 2193 users of PPI, 5950 users of the hydroxychloroquine, 1816 users of famotidine and 26,820 non-famotidine users. After PS stratification, the hazard ratios for death were as follows: famotidine vs no famotidine HR 1.03 (0.89-1.18); vs PPIs: HR 1.14 (0.94-1.39); vs hydroxychloroquine:1.03 (0.85-1.24). Similar results were observed for the risk of death or intensive services use.

Conclusion

We found no evidence of a reduced risk of COVID-19 outcomes among hospitalized COVID-19 patients who used famotidine compared to those who did not or compared to PPI or hydroxychloroquine users.
RNA-bound PGC-1α controls gene expression in liquid-like nuclear condensates
Authors: Pérez-Schindler Joaquín , Kohl Bastian , Schneider-Heieck Konstantin , Adak Volkan , Delezie Julien , Maier Geraldine , Sakoparnig Thomas , Vargas-Fernández Elyzabeth , Karrer-Cardel Bettina , Ritz Danilo , Schmidt Alexander , Hondele Maria , Hiller Sebastian , Handschin Christoph
Published: September 2020

The peroxisome-proliferator-activated receptor-γ coactivator-1α (PGC-1α) integrates environmental cues by controlling complex transcriptional networks in various metabolically active tissues. However, it is unclear how a transcriptional coregulator coordinates dynamic biological programs in response to multifaceted stimuli such as endurance training or fasting. Here, we discovered a central function of the poorly understood C-terminal domain (CTD) of PGC-1α to bind RNAs and assemble multi-protein complexes. Surprisingly, in addition to controlling the coupling of transcription and processing of target genes, RNA binding is indispensable for the recruitment of PGC-1α to chromatin into liquid-like nuclear condensates, which compartmentalize and regulate active transcription. These results demonstrate a hitherto unsuspected molecular mechanism by which complexity in the regulation of large transcriptional networks by PGC-1α is achieved. These findings are not only essential for the basic understanding of transcriptional coregulator-driven control of biological programs, but will also help to devise new strategies to modulate these processes in pathological contexts in which PGC-1α function is dysregulated, such as type 2 diabetes, cardiovascular diseases or skeletal muscle wasting.
SpRY greatly expands the genome editing scope in rice with highly flexible PAM recognition
Authors: Xu Ziyan , Kuang Yongjie , Ren Bin , Yan Daqi , Yan Fang , Spetz Carl , Sun Wenxian , Wang Guirong , Zhou Xueping , Zhou Huanbin
Published: September 2020

Plant genome engineering mediated by various CRISPR-based tools requires specific protospacer adjacent motifs (PAMs), such as the well-performed NGG, NG, NNG,etc., to initiate the target recognition, which notably restricts the editable range of the plant genome. In this study, we thoroughly investigated the nuclease activity and the PAM preference of two structurally-engineered SpCas9 variants (SpG and SpRY) in transgenic rice. Our study shows that SpG nuclease favors NGD PAMs, albeit less efficiently than the previously described SpCas9-NG and that SpRY nuclease achieves efficient editing across a wide range of genomic loci, exhibiting a preference of NGD as well as NAN PAMs. Furthermore, SpRY-fused cytidine deaminase hAID*Δ and adenosine deaminase TadA8e were generated, respectively. These constructs efficiently induced C-to-T and A-to-G conversions in the target genes toward various non-canonical PAMs, including non-G PAMs. Remarkably, high-frequency self-editing events (indels and DNA fragments deletion) in the integrated T-DNA fragments as a result of the nuclease activity of SpRY were observed, whereas the self-editing of SpRY nickase-mediated base editor was quite low in transgenic rice lines. In conclusion, the broad PAM compatibility of SpRY greatly expands the targeting scope of CRISPR-based tools in plant genome engineering.
Differential dopaminergic modulation of spontaneous cortico-subthalamic activity in Parkinson’s disease
Authors: Sharma Abhinav , Vidaurre Diego , Vesper Jan , Schnitzler Alfons , Florin Esther
Published: September 2020

Pathological oscillations including elevated beta activity in the subthalamic nucleus (STN) and between STN and cortical areas are a hallmark of neural activity in Parkinson’s disease (PD). Oscillations also play an important role in normal physiological processes and serve distinct functional roles at different points in time. We characterised the effect of dopaminergic medication on oscillatory whole-brain networks in PD in a time-resolved manner by employing a hidden Markov model on combined STN local field potentials and magnetoencephalography (MEG) recordings from 17 PD patients. Dopaminergic medication led to coherence within the medial and orbitofrontal cortex in the delta/theta frequency range. This is in line with known side effects of dopamine treatment such as deteriorated executive functions in Parkinson’s disease. In addition, dopamine caused the beta band activity to switch from an STN-mediated motor network to a frontoparietal-mediated one. In contrast, dopamine did not modify local STN-STN coherence in PD. STN–STN synchrony emerged both on and off medication. By providing electrophysiological evidence for the differential effects of dopaminergic medication on the discovered networks, our findings open further avenues for electrical and pharmacological interventions in PD.
Prevalence of alternative AUG and non-AUG translation initiators and their regulatory effects across plants
Authors: Li Ya-Ru , Liu Ming-Jung
Published: September 2020

Translation initiation is a key step determining protein synthesis. Studies have uncovered a number of alternative translation initiation sites (TISs) in mammalian mRNAs and showed their roles in reshaping the proteome. However, the extent to which alternative TISs affect gene expression across plants remains largely unclear. Here, by profiling initiating ribosome positions, we globally identified in vivo TISs in tomato and Arabidopsis and found thousands of genes with more than one TIS. Of the identified TISs, >19% and >20% were located at unannotated AUG and non-AUG sites, respectively. CUG and ACG were the most frequently observed codons at non-AUG TISs, a phenomenon also found in mammals. In addition, although alternative TISs were usually found in both orthologous genes, the TIS sequences were not conserved, suggesting the conservation of alternative initiation mechanisms but flexibility in using TISs. Unlike upstream AUG TISs, the presence of upstream non-AUG TISs was not correlated with the translational repression of main open reading frames, a pattern observed across plants. Also, the generation of proteins with diverse N-terminal regions through the use of alternative TISs contributes to differential subcellular localization, as mutating alternative TISs resulted in the loss of organelle localization. Our findings uncovered the hidden coding potential of plant genomes and, importantly, the constraint and flexibility of translational initiation mechanisms in the regulation of gene expression across plant species.
Twinning in SnO2-based ceramics doped with CoO and Nb2O5: morphology of multiple twins revealed by electron backscatter diffraction
Authors: Padrón-Navarta José Alberto , Barou Fabrice , Daneu Nina
Published: September 2020

Electron backscatter diffraction (EBSD) was used for the analysis of multiple cyclic twins in cassiterite (SnO2), which form during sintering of SnO2with small additions of CoO and Nb2O5. Grain misorientation analysis has shown that about one third of all grains contain {101} twin boundaries (TBs). The majority of these grains are contact twins, whereas a small fraction of grains are multiple, mainly cyclic twins. A procedure was developed inMTEX[Bachmann, Hielscher & Schaeben (2010).Solid State Phenom.160, 63–88] for automated identification of crystallographically different types of cyclic twins and found two main types: coplanar twins composed of three or four domains with a common [010] axis and alternating twins composed of three to seven domains oriented along the [111] axis. Both types of cyclic twins have a characteristic common origin (nucleus) of all TBs, which is positioned eccentric relative to the grain section and the cycle is closed with a shorter non-crystallographic contact between the first and the last twin domain. The morphology of cyclic twins suggests that they form by nucleation in the initial stages of grain growth. The average size of twinned grains increases with the number of twin domains indicating the influence of TBs formation on the growth of composite grains.
Triple molybdates K3–x
Na1+x

M
4(MoO4)6 (M = Ni, Mg, Co) and K3+x
Li1–x
Mg4(MoO4)6 isotypic with II-Na3Fe2(AsO4)3 and yurmarinite: synthesis, potassium disorder, crystal chemistry and ionic conductivity
Authors: Gulyaeva Oksana A. , Solodovnikova Zoya A. , Solodovnikov Sergey F. , Zolotova Evgeniya S. , Mateyshina Yuliya G. , Uvarov Nikolai F.
Published: September 2020

The triple molybdates K3–x
Na1+x

M
4(MoO4)6 (M = Ni, Mg, Co) and K3+x
Li1–x
Mg4(MoO4)6 were found upon studying the corresponding ternary molybdate systems, and their structures, thermal stability and electrical conductiviplusmnty were investigated. The compounds crystallize in the space group R
3
c and are isostructural with the sodium-ion conductor II-Na3Fe2(AsO4)3 and yurmarinite, Na7(Fe3+, Mg, Cu)4(AsO4)6; their basic structural units are flat polyhedral clusters of the central M1O6 octahedron sharing edges with three surrounding M2O6 octahedra, which combine with single NaO6 octahedra and bridging MoO4 tetrahedra to form open three-dimensional (3D) frameworks where the cavities are partially occupied by disordered potassium (sodium) ions. The split alkali-ion positions in K3–x
Na1+x

M
4(MoO4)6 (M = Ni, Mg, Co) give their structural formulae as [(K,Na)0.5□0.5)]6(Na)[M1][M2]3(MoO4)6, whereas the lithium-containing compound (K0.5□0.5)6(Mg0.89K0.11)(Li0.89Mg0.11)Mg3(MoO4)6 shows an unexpected (Mg, K) isomorphism, which is similar to (Mn, K) and (Co, K) substitutions in isostructural K3+x
Li1–x

M
4(MoO4)6 (M = Mn, Co). The crystal chemistry of the title compounds and related arsenates, phosphates and molybdates was considered, and the connections of the cationic distributions with potential 3D ionic conductivity were shown by means of calculating the bond valence sum (BVS) maps for the Na+, Li+ and K+ ions. Electrical conductivity measurements gave relatively low values for the triple molybdates [σ = 4.8 × 10−6 S cm−1 at 390°C for K3NaCo4(MoO4)6 and 5 × 10−7 S cm−1 at 400°C for K3LiMg4(MoO4)6] compared with II-Na3Fe2(AsO4)3 (σ = 8.3 × 10−4 S cm−1 at 300°C). This may be explained by a low concentration of sodium or lithium ions and the blocking of their transport by large potassium ions.