bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carbon Stock Variation along altitudinal gradient of Wacho Forest in Hawa Galan District, Kellem Wollega Zone, Oromia Region, Ethiopia
Authors: Gashu Gezahegn , Gidey Gebre , Deressa Sime , Fekansa Zame , Awoke Halid 
Published: July 2020

Abstract
Background

Forest ecosystem plays a crucial role in the global carbon cycle; as such, mitigating high atmospheric concentrations of carbon dioxide and other greenhouse gases by naturally taking carbon from the atmosphere through photosynthesis. Verification and accounting of carbon stock in forest ecosystem have been renowned as a potential strategy to reduce and stabilize atmospheric concentrations of greenhouse gas. Forest sequesters and store more carbon than any other terrestrial ecosystem and it is an important natural break on climate change. It acts as a carbon reservoir by storing large amount of carbon in trees, undergrowth vegetation, forest floor and soil.
Result

The mean carbon stock of each carbon pool was changed along altitudinal class of the study area. The largest mean above and below ground carbon stock was found in the second altitudinal class(1560.01-1643m) followed by first altitudinal class(1435-1560m) and the third altitudinal class (1643.01-1704m) of the study area. The largest mean dead tree and dead wood carbon stock was also stored in the first altitudinal class followed by the third and the second altitudinal class of the study area. The largest mean litter carbon stock was found in the first altitudinal class followed by the second and the third altitudinal class of the study area. The largest mean soil organic carbon was found in the third altitudinal class followed by the second and the first altitudinal class of the study area.
Conclusions

The carbon stock variation along altitudinal gradients indicated that, altitude had no a statistically significant effect on any of the carbon pools except litter carbon of the study area at 95% of confidence interval.
P2X7 receptor/NLRP3 inflammasome complex and a-synuclein/parkin&nbsp;balance in neo-diagnosed, treatment-naïve Parkinson disease: a prospective study
Authors: Solini Anna , Rossi Chiara , Santini Eleonora , Giuntini Martina , Raggi Francesco , Parolini Federico , Biancalana Edoardo , Prete Eleonora Del , Bonuccelli Ubaldo , Ceravolo Roberto 
Published: July 2020

Abstract
Background

Neuro, and likely systemic inflammation, with abnormal α-synuclein deposition, participate in the development of Parkinson’s disease (PD). The P2 × 7 receptor/NLRP3 inflammasome complex is upregulated in the brain of PD patients. Aim of this study was to explore whether the systemic activation of such complex might participate in the pathogenesis of PD.
Methods

Systemic expression and functional activity of the inflammasome were measured in 25 newly diagnosed PD patients and 25 controls at baseline and after twelve months of pharmacologic treatment, exploring the involved intracellular signalling and its epigenetic regulation. A putative mechanistic explanation of the results was validated in a murine model of neuroinflammation.
Results

De-novo PD patients were characterized by a systemic hyper-expression of the P2 × 7R/NLRP3 inflammasome platform, likely modulating circulating and lymphomonocyte α-synuclein, whose deposits represent the main pathogenetic factor of PD. A reduced JNK phosphorylation might be the involved intracellular signalling. miR-7 and miR-30, implied in the pathogenesis of PD and in the post-transcriptional control of α-synuclein and NLRP3 expression, were also increased in PD. After one year of usual anti-Parkinson treatments, such inflammatory platform was significantly reduced. In the substantia nigra of P2 × 7R KO mice, a neuroinflammatory stimulus induced a strong expression of parkin, a protective protein, suggesting that P2 × 7R activation might participate in the inflammatory damage occurring in specific brain areas also by inhibiting parkin expression.
Conclusion

Newly-diagnosed PD subjects display a systemic hyper-expression of the P2 × 7R/NLRP3 inflammasome platform that seems to modulate circulating and lymphomonocyte α-synuclein; a reduced JNK phosphorylation might be the intracellular signalling mediating this effect, undergoing an epigenetic regulation by miR-7 and miR-30.
Trial registration
ClinicalTrials.gov (NCT03918616).
Prevalence of Carriage of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae Among Pregnant Women in the Primary Health Care Center and Hospital Setting in Indonesia
Authors: Oktaviani Rochmanah , Hasanah Miratul , Setyarini Wahyu , Parathon Hari , Kitagawa Koichi , Nakanishi Noriko , Nomoto Ryohei , Osawa Kayo , Kinoshita Shohiro , Hirai Itaru , Shirakawa Toshiro , Kuntaman K 
Published: July 2020

Abstract
Background: The incidence of healthy individuals carrying Extended-Spectrum Beta-Lactamase producing Enterobacteriaceae (ESBL-E), especially E. coli (ESBL-EC) and Klebsiella pneumoniae (ESBL-KP), is increasing worldwide. ESBL-E causes early or late onset of neonatal sepsis, resulting in increased morbidity and mortality rates. Although maternal-neonatal transmissions of ESBL-E have been reported in several countries, the prevalence of ESBL-E carriage among pregnant women in Indonesia is not clear. In the present study, we compared the prevalence of carriage of ESBL-E among pregnant women in a primary health care center (PHC) versus two hospitals in Indonesia and identified the phenotypic and genotypic characteristics of the isolated ESBL-E strains. Methods: We collected rectal swab samples from 200 pregnant women who visited a PHC (101 women) or were admitted to Dr. Soetomo Referral Hospital or Airlangga University Hospital (99 women) in Surabaya, Indonesia from July to October 2018. The samples were cultivated on MacConkey Agar plates supplemented with cefotaxime 2 mg/L, at 37oC overnight. The isolated strains were identified by Bruker MALDI BiotyperÒ System, phenotypic detection of ESBL was performed by the combination disk method, and antibiotic susceptibility was tested by the disk diffusion method. In addition, ESBL gene was identified by PCR and DNA sequencing and molecular epidemiological studies were performed by PFGE. Results: ESBL-E strains were isolated from 25 (rate of fecal carriage; 24.8%) pregnant women who visited the PHC and 49 (49.5%) pregnant women who were admitted to the hospitals. The rate of ESBL-E carriage of pregnant women in the hospitals was significantly higher than that in the PHC. Among the 74 isolated ESBL-E strains, ESBL-EC was most frequently isolated (62 strains), followed by ESBL-KP (12 strains). In addition, blaCTX-M15 was the most frequent ESBL gene type of the isolated ESBL-E strains. Conclusion: Our results revealed the high prevalence of ESBL-E carriage in pregnant women, especially those who were admitted to the hospitals. CTX-M15 ESBL-EC was the most frequent type of ESBL-E in the pregnant women in our study. Continuous surveillance for ESBL-E carriage in pregnant women is strongly recommended to reduce the incidence of neonatal sepsis in Indonesia.
A novel cell permeability assay for macromolecules
Authors: Bueso Yensi Alejandra Flores , Walker Sidney Peter , Tangney Mark 
Published: July 2020

Abstract
Background
Many cell permeabilisation methods to mediate internalisation of various molecules to mammalian or bacterial cells have been developed. However, no size-specific permeability assay suitable for all cells exists.
Results
We report for the first time, use of intrinsically biotinylated cell components as the target for reporter molecules for assessing permeabilisation. Due to its well-described biotin binding activity, we developed an assay using Streptavidin (SAv) as a molecular weight marker for assessing eukaryotic and prokaryotic cell internalisation, using flow cytometry as a readout. This concept was tested here in the development of host DNA depletion strategies for microbiome analysis of formalin-fixed samples. This strategy requires differential cell permeabilisation, where mammalian cells but not bacterial cells are permeabilised, and are subsequently treated with a nuclease. Here, the internalisation of a SAv-conjugate was used as a reference for nucleases of similar dimensions. With this assay, it was possible to demonstrate that FF does not generate pores which allow the introduction of 60 KDa molecules in both mammalian and bacterial membranes/envelopes. Among surfactants tested, Saponin showed the best selectivity for mammalian cell permeabilisation, which, when coupled with Benzonase nuclease, provided the best results for host DNA depletion, representing a new host depletion strategy for formalin fixed samples.
Conclusion
The assay presented provides researchers with a sensitive and accessible tool for discerning membrane/cell envelop permeability for different size macromolecules.
The role of carbon ion radiotherapy for unresectable locally recurrent rectal cancer: a single institutional experience
Authors: Cai Xin , Du Yueyao , Wang Zheng , Li Ping , Yu Zhan , Zhang Qing , zhang zhen 
Published: July 2020

Abstract
Background
Treatment for locally recurrent rectal cancer after surgery is still a challenge. With the physical and biological advantages, carbon-ion radiotherapy (CIRT) could be a choice for these patients. The purpose of this study was to investigate the efficacy and safety of CIRT for unresectable locally recurrent rectal cancer in Chinese patients.
Methods
Date from 25 patients with unresectable locally recurrent rectal cancer treated by CIRT from July 2015 to April 2019 were analyzed retrospectively. The endpoints of this study were overall survival (OS), local control (LC) and acute and late toxicity.
Results
With the median follow-up of 19.6 (range 5.1–52.5) months, data of all 25 patients were collected. Median prescribed dose for tumor was 72 Gy (relative biologic efficacy (RBE)) (range 48-75.6 Gy (RBE)). The LC rates at 1 and 2 years were 90.4% and 71.8%. Overall LC at 1- and 2-year were 76.2% and 30.5% for 9 patients whose prescribed tumor doses of CIRT < 66 Gy (RBE), 100% and 100% for 16 patients whose prescribed doses of CIRT ≥ 66 Gy (RBE). Patients received ≥ 66 Gy (RBE) had obviously better LC rates than those received < 66 Gy (RBE) (P = 0.001). The OS rates at 1 and 2 years were 82.9% and 65.1%, respectively. No acute toxicity over grade 2 was observed, grade 3 late toxicity were observed in 3 patients: gastrointestinal toxicity (n = 1), neuropathy (n = 1), pelvic infection (n = 1). No Grade 4 or higher toxicity was observed.
Conclusion
Our study shows that CIRT is effective for unresectable locally recurrent rectal cancer patients with acceptable toxicity.
Per-Fraction Positional and Dosimetric Performance of Prone Breast Tangential Radiotherapy Assessed with Daily Rapid Kilo-voltage Cone Beam Computed Tomography: Key Statistics, Predictors, and Recommendations
Authors: Yoon Suk Whan , Taunk Neil K , Freedman Gary M , Hubley Emily , O'Reilly Shannon , Teo Boon-Keng K , Anamalayil Shibu , Dong Lei , Kennedy Christopher , Zou Wei , Metz James M , Li Taoran 
Published: July 2020

Abstract
Background
This study investigates daily breast geometry and delivered dose to prone-positioned patients undergoing tangential whole breast radiation therapy (WBRT) on an O-ring linear accelerator with 6X flattening filter free mode (6X-FFF), planned with electronic compensation (ECOMP) method. Most practices rely on skin marks or daily planar image matching for prone breast WBRT. This system provides low dose daily CBCT, which was used to study daily robustness of delivered dose parameters for prone-positioned WBRT.
Methods
Eight patients treated with 16-fraction prone-breast WBRT were retrospectively studied. Planning CTs were deformed to daily CBCT to generate daily synthetic CTs, on which delivered dose distributions were calculated. A total of 8 × 16 = 128 synthetic CTs were generated. Consensus ASTRO definition was used to contour Breast PTV Eval for each daily deformed CT. Breast PTV Eval coverage (V90%) and hotspot (V105% and Dmax) were monitored daily to compare prescription dose with daily delivered dose. Various predictors including patient weight, breast width diameter (BWD), and Dice similarity coefficient (DSC) were fit into an analysis of covariance model predicting V90% and V105% deviation from prescribed (ΔV90%, ΔV105%). Statistical significance is indicated with asterisks (* for p < 0.05; ** for p < 0.001).
Results
Daily delivered Breast PTV Eval V90% was moderately smaller than prescribed (median ΔV90%=-0.1%*), while V105% was much larger (median ΔV105%=+10.1%** or + 92.4cc**). Patient’s weight loss correlated with significantly increased ΔV105% (+ 4.6% / -1% weight., R2 = 0.4**) and moderately decreased ΔV90% (-0.071%/-1% wt., R2 = 0.2**). Comprehensive ANCOVA models indicated three factors affect ΔV90% and ΔV105% the most: (1) BWD decrease (-0.09%* and + 10%**/-1cm respectively), (2) PTV Eval volume decrease (-0.4%** and + 9%**/-100 cc), and for ΔV105% only, (3) the extent of breast deformation (+ 10%**/-0.01 DSC). Breast PTV Eval volume also decreased with time (-2.21*cc/fx), possibly indicating seroma resolution and increase in V105% over time.
Conclusions
Daily CBCT revealed key delivered dose parameters vary significantly for patients undergoing tangential prone breast WBRT planned with ECOMP using 6X-FFF. Patient weight, BWD, and breast shape deformation could be used to predict dosimetric variations from prescribed. Preliminary findings suggest an adaptive plan based on daily CBCT could reduce excessive dose to the breast.
Effect of inhaled anesthetics gases on cytokines and oxidative stress alterations for the staff health status in hospitals
Authors: Al-Rasheedi Khaled , Alqasoumi Abdulmajeed , Emara Ashraf 
Published: July 2020

Abstract
Background

Waste anesthetic gases are few amounts of inhalational anesthesia that escape during its administration. Waste anesthetic gases such as sevoflurane and nitrous oxide can induce toxic effects among health team members working in hospitals. The objective of this study was to identify the harmful effects of upon the waste anesthetic gases exposure on oxidative stress and cytokines of health team members working in hospitals.
Methods

This study involved a control group and waste anesthetic gases exposure group. The exposed group was divided into six subgroups (Surgeons; Surgeon's assistants; Anaesthesiologists; Anesthesiologists' assistants; Nurses and Workers). Serum fluoride, tumor necrosis alpha, interleukin 2 and plasma malondialdehyde, catalase, glutathione peroxidase and superoxide dismutase activities were measured.
Results

A significant elevation was detected in fluoride, tumor necrosis alpha and interleukin 2 levels in anesthesia specialists and anesthesia assistances as compared with the surgeon, surgeon assistants, nurses and workers groups. On the other hand; a significant elevation in levels of malondialdehyde and a significant decline in levels of glutathione peroxidase, catalase and superoxide dismutase in surgeon group as compared with other exposed groups. However, a significant elevation was detected in serum interleukin 4 level among anesthesia specialists as compared with exposed groups.
Conclusions

Exposure to waste anesthetic gases explained a high prevalence of morbidity among operating room personnel which was observed in the present study due to exposure to oxidative stress and cytokines storm. Oxidative stress and inflammatory cytokines are responsible for induction or progression of some diseases. The studied groups (anesthesia specialists and anesthesia assistances) had exposure to high levels of waste anesthetic gases and were more risky to its toxic effects. Accordingly, an education program should be focusing on how to manage these gases to reduce its toxic effects on health staff, and continuous effort evaluating the safety of anesthesia in various aspects is required.
Anaemia is Associated with Severe Illness in COVID-19: A Retrospective Cohort Study
Authors: Tao Zheying , Liu Mingyu , Wu Jingyi , Xu Jing , Chen Wei , Yang Zhitao , Xu Xiaoman , Liu Ling , Chen Ruwu , Xie Jingyuan , Wang Huiming , Liu Jialin 
Published: July 2020

Abstract
Background and objective:Anaemia commonly aggravates the severity of respiratory diseases, whereas thus far, no study has elucidated the impact of anaemiaonCorona Virus Disease 2019(COVID-19). The aim of this study was to evaluate the clinical characteristics of patients with anaemia, and to further explore the relationship between anaemiaand the severity of COVID-19.METHODS:In this single-center, retrospective, observational study, a total of 222 patients were recruited, including 79 patients with anaemia and 143 patients without anaemia. Clinical characteristics, laboratory findings, disease progression and prognosis were collected and analyzed. Risk factors associated with the severe illness in COVID-19were established by univariable and multivariable logistic regression models.Result：In our cohort, compared to patients without anaemia, patients with anaemia were more likely to experience one or more comorbidities and severe COVID-19 illness, as well as higher mortality. More patients demonstrated elevated levels of C-reactive protein (CRP), procalcitonin(PCT) and creatinine in anaemia group. Levels of erythrocyte sedimentation rate(ESR), D-dimer, myoglobin, T-pro brain natriuretic peptide(T-pro-BNP) and urea nitrogen(BUN)in patients with anaemia were significantly higher than those without. In addition,the proportion of patients with dyspnoea，elevated CRP and PCT was positively associated with the severity of anaemia. The Odd Ratio (OR) of anaemia related to the severe condition of COVID-19 was 5.07 (95% CI:1.82-14.18, P=0.002) and 3.47 (95% CI:1.02-11.75, P=0.046) after adjustment for baseline date and laboratory indices, respectively.Conclusion:Anaemia is an independent risk factor associated with the severe illness of COVID-19, and healthcare professionals should be more sensitive to the haemoglobin levels of COVID-19 patients on admission. To avoid rapid deterioration, more intensive care should be given to patients with anaemia.Trial registration: Ethics committee of Wuhan University People's Hospital (wdry2020-k064)
A Solitary Giant Neurofibroma of Inguinal Region—A Case Report
Authors: Zhou Haiying , Lu Hui 
Published: July 2020

Abstract
Background:Neurofibroma is a rare nerve sheath tumorofneuroectodermal origin, especially the huge and isolated neurofibroma located in the inguinal region. To our knowledge, no such case has previously been reported.Case presentation:We report a case of 34-year-old male patient with a 4-year history of progressive enlargement of the medial root mass in his left thigh with sitting and standing disorders along with pain. The tumor was completely removed by operation, and pathological diagnosisshowed neurofibroma. There was no obvious neurologic defect after surgery, and no recurrence tendency was found in the follow-up of 2years.Conclusions:For a large solitary mass with slow growth and no malignant clinical manifestations for a long time, clinicians can not rule out the hypothetical diagnosis of neurofibroma, even though its growth site is very rare, such as this case of a huge tumor located in the groin. For neurogenic tumors, early operation should be performed, and the prognosis of patients after tumor resection isexcellent.
Health related quality of life among end stage renal disease patients from low income country, Nepal: a cross sectional study using WHOQOL-BREF
Authors: Ranabhat Kamal , Khanal Pratik , Mishra Shiva Raj , Khanal Anu , Tripathi Sangita , Sigdel Mahesh Raj 
Published: July 2020

Abstract
Background
Little is known about the health-related quality of life (HRQOL) among end stage renal diseases (ESRD) patients in Nepal. This study examined the health-related quality of life of among the dialysis and transplant patients in Nepal.
Methods
Nepali Version of WHOQOL-BREF questionnaire was administered using face to face interviews among ESRD patients, from two large national referral centers in Nepal. The differences in socio-demographic characteristics among ESRD patients were examined using Chi-square test. The group differences in QOL were examined using Mann-Whitney U test and Kruskal-wallis tests.
Results
Of the 161 participants, 92 (57.1%) were transplant patients and 62 (42.9%) were dialysis patients. Hypertension (70.9%) was the commonest co-morbidity among ESRD patients. Dialysis patients scored significantly lower than the transplant patients in all the four domains as well as in overall perception of quality of life and general health. Ethnicity (p = 0.020), socio-economic status (p < 0.001), educational status (p < 0.001) and employment status (p = 0.009) was significantly associated with the overall QOL in ESRD patients. Across patient groups, educational status (p = 0.012) was positively significant with the QOL in dialysis patients while residence (p = 0.023), socio-economic status (p < 0.001), educational status (p = 0.004) and diabetes status (p = 0.010) was significantly associated with the QOL in transplant patients.
Conclusion
The overall QOL of the renal transplant recipient was higher than those of the patients on maintenance hemodialysis; this was true in all the four domains of the WHOQOL-BREF. ESRD patient with low HRQOL should be prioritized for risk modification intervention.
Nonlinear Ridge Regression Improves Robustness of Cell-Type-Specific Differential Expression Studies
Authors: Takeuchi Fumihiko , Kato Norihiro 
Published: July 2020

Abstract
Background: Epigenome-wide association studies (EWAS) and differential gene expression analyses are generally performed on tissue samples, which consist of multiple cell types. Cell-type-specific effects of a trait, such as disease, on the omics expression are of interest but difficult or costly to measure experimentally. By measuring omics data for the bulk tissue, cell type composition of a sample can be inferred statistically. Subsequently, cell-type-specific effects are estimated by linear regression that includes terms representing the interaction between the cell type proportions and the trait. This approach involves two issues, scaling and multicollinearity.Results: First, although cell composition is analyzed in linear scale, differential methylation/expression is analyzed suitably in the logit/log scale. To simultaneously analyze two scales, we developed nonlinear regression. Second, we show that the interaction terms are highly collinear, which is obstructive to ordinary regression. To cope with the multicollinearity, we applied ridge regularization. In simulated and real data, the improvement was modest by nonlinear regression and substantial by ridge regularization. Conclusion: Nonlinear ridge regression performed cell-type-specific association test on bulk omics data more robustly than previous methods. The omicwas package for R implements nonlinear ridge regression for cell-type-specific EWAS, differential gene expression and QTL analyses. The software is freely available from https://github.com/fumi-github/omicwas