bluuebunny/crossref_metadata_2025_split huggingface dataset:
“Side effects-part of the package” – A mixed methods approach to adverse events among patients with DR-TB under RNTCP Gujarat, India
Authors: Jakasania Arjunkumar Hardas , shringarpure Kalpita , Kapadia Dixit , Sharma Radhika , Mehta Kedar , Prajapati Arpit , Soundappan Kathirvel 
Published: March 2020

Abstract
Background Unsuccessful treatment outcomes among patients with drug resistant tuberculosis (DR-TB) are associated with poor treatment adherence due to high rates of adverse events (AEs). However, AEs are not systematically collected and managed under programmatic setting. The present study aims to assess the a) incidence and pattern of adverse events in first three months of DR-TB treatment; b) treatment seeking behaviour for AE management; and c) explore the challenges perceived by patients and healthcare providers in seeking treatment/reporting AEs. Methods This mixed methods study included all patients diagnosed and initiated on treatment during July-September 2018 at Ahmedabad DR-TB centre under RNTCP. The patients were interviewed telephonically and assessed for all AEs experienced by them during first three months of DR-TB treatment initiation. In-depth interviews and key-informant interviews were conducted among patients and DOTS supervisors, and programme staff (treatment supervisors, Medical Officer and District Program Manager). Results Total 207 AEs were reported by the 74 DR-TB patients who were interviewed. All patients experienced at least one AE during treatment. Incidence rate of AEs (experienced) was 3.11 (1 st month-4.6, 2 nd month-2.7, 3 rd month-2.02) per 100 person days of the 207 AEs, gastro-intestinal (59, 28.3%), ophthalmic (32, 15.4%) and otolaryngology (25, 11.9%) system related AEs were commonly experienced. Treatment was not sought in two-fifths of the AEs. Themes and subthemes related to challenges in treatment seeking or reporting of AEs were 1) Patient related-Misconceptions, accessibility and affordability of management, lack of counselling support, stigma and discrimination, past treatment experience; 2) Health system related- lack of guideline and training for AE management, poor coordination between hospital and tuberculosis centre.Conclusion The incidence of AEs was high among patients with DR-TB in the first three months of treatment and treatment seeking/reporting was low. Adequate health education and counselling of the patient should be done at initiation of treatment. An efficient real-time reporting and management of AE can be developed and tested for effective DR-TB control.
Haplotyping by linked-read sequencing (HLRS) of the genetic disease carriers for preimplantation genetic testing without a proband or relatives
Authors: Li Qing , Mao Yan , Li Shaoying , Du Hongzi , He Wenzhi , He Jianchun , Kong Lingyin , Zhang Jun , Liang Bo , Liu Jianqiao 
Published: March 2020

Abstract
Background: In order to mitigate the risk of allele dropout (ADO) and ensure the accuracy of preimplantation genetic testing for monogenic disease (PGT-M), it is necessary to construct parental haplotypes.. Typically, haplotype resolution is obtained by genotyping multiple polymorphic markers in both parents and a proband or a relative. Sometimes, single sperm typing, or tests on the polar bodies may also be useful. Nevertheless, this process is time-consuming. At present, there was no simple linkage analysis strategy for patients without affected relatives.Method: To solve this problem, we established a haplotyping by linked-read sequencing (HLRS) method without the requirement for additional relatives. First, the haplotype of the genetic disease carriers in the family was constructed by linked-read sequencing, and then the informative single nucleotide polymorphisms (SNPs) in upstream and downstream mutation region were selected to construct the embryo haplotype and to determine whether the embryo was carrying the mutation. Two families were selected to validate this method; one with alpha thalassemia and the other with NDP gene disorder.Results: The haplotyping by linked-read sequencing (HLRS) method was successfully applied to construct parental haplotypes without recruiting additional family members; the method was also validated for PGT-M. The mutation carriers in these families were sequenced by linked-read sequencing, and their haplotypes were successfully phased. Adjacent SNPs of the mutation gene were identified. The informative SNPs were chosen for linkage analyses to identify the carrier embryos. For the alpha thalassemia family, a normal blastocyst was transferred to the uterus and the accuracy of PGT-M was confirmed by amniocentesis at 16 weeks of gestation. Conclusions: Our results suggest that HLRS can be applied for PGT-M of monogenic disorders or de novo mutations where the mutations haplotype cannot be determined due to absence of affected relatives. Keywords: Preimplantation Genetic Testing for monogenic disease, Linked-read sequencing, Linkage analyses, Haplotype
Validation of the French version of the McLean Screening Instrument for Borderline Personality Disorder (MSI-BPD)
Authors: Pham-Scottez Alexandra , Mirkovic Bojan , Cailhol Lionel , Guelfi Julien-Daniel , Perez-Diaz Fernando , Speranza Mario , Corcos Maurice , Zanarini Mary 
Published: March 2020

Abstract
Background The study examines the psychometric properties of the French version of the McLean Screening Instrument for Borderline Personality Disorder (MSI-BPD) created by M. Zanarini to screen borderline personality disorder in clinical and non-clinical populations. Method In this multicentric longitudinal study from the European Network on Borderline Personality Disorder, a sample of 85 adolescent patients from five psychiatric centres and 85 matched controls without psychiatric comorbidity completed the MSI-BPD, French version, and were interviewed with the Structured Interview for DSM-IV Personality (SIDP-IV), in order to assess the presence or absence of borderline personality disorder. Results The MSI-BPD showed excellent internal consistency (α = 0.87 [0.84;0.90]). Compared to the semi-structured reference interview (SIDP-IV), the MSI-BPD showed substantial congruent validity (AUC = 0.93, CI 95%: 0.90 - 0.97). The optimal cut-off point in the present study was 5 or more as it had relatively high sensitivity (0.87) and specificity (0.85). In our sample, the cut-off point (7 or more) proposed by the original developers of the MSI-BPD showed high specificity (0.95) but low sensitivity (0.63). Conclusions The French version of the MSI-BPD is now available, and its psychometric properties are satisfactory. The French version of the MSI-PBD can be used as a screening tool for borderline personality disorder, for clinical purposes or in research studies.
High level of contamination of antimicrobial drug resistant non-typhoidal Salmonella enterica in commercial poultry and its surroundings in Chitwan, Nepal
Authors: Nelson Amy , Manandhar Sulochana , Ruzante Juliana , Gyawali Arrogya , Dhakal Bimala , Dulal Santosh , Chaulagai Rupendra , Dixit Sameer M 
Published: March 2020

Abstract
BackgroundAntimicrobial resistance (AMR) among bacterial pathogens is a fast-growing public health concern. AMR in non-typhoidal Salmonella species among food animals is of special concern as this may transmit resistant pathogens to humans during handling or consumption of animal products. In Nepal, the possibility of AMR Salmonella species among food animals is an important area of research, particularly in light of the rapidly growing poultry industry, lack of surveillance, and paucity of studies that have been conducted. MethodsTaking one health approach, a cross-sectional study was carried out in Chitwan district of Nepal between May and October 2017. Various environmental samples viz. farm litter, feed, water, poultry feces, vehicle swabs, farm swabs from 12 broiler poultry farms and various sections of poultry carcasses from 21 slaughter houses were aseptically collected. These were microbiologically assessed for the presence of non-typhoidal Salmonella and their phenotypic and genotypic indicators of antimicrobial resistance. ResultsOverall, Of 62 environmental samples collected, 31(50%) tested positive for Salmonella enterica serovars with environmental swabs (70%, 8/12) being the most culture positive sample types. Similarly, of 159 tissue samples collected from 24 carcasses, 79% (126/159) were culture positive for Salmonella enterica. Nearly 97% (153/157), 11% (17/157), 5% (8/157) and none of isolates showed resistance to tetracycline, ciprofloxacin, azithromycin and meropenem respectively. Some 83% (131/157), 40% (64/157), 8% (13/157) and 0.6% (1/157) of isolates tested positive for tetA, QrnS, mefA and VIM-1 AMR genes corresponding to the above antimicrobials respectively.ConclusionsThis study revealed gross contamination of farms and subsequent poultry meat samples with Salmonella enterica serovars that were resistant to several clinically applicable antimicrobials. This reinforces an urgent need to implement proper biosecurity approaches from farms to slaughter houses and strengthen policies to cease the rampant use of clinically important antimicrobials in poultry.
Transport of Goods Powered by Cereal Straw: Temporal and Spatial Biomass Availability for Future Bio-LNG Production in Germany
Authors: Brosowski André , Bill Ralf , Thrän Daniela 
Published: March 2020

Abstract
Background: Half of the UN climate target for 2030 has been achieved and further progress requires swiftly implementable solutions. In this context, the fermentation of cereal straw is a promising option. Returning the digestate to the farmland can close agricultural cycles while simultaneously producing biomethane for the transport sector. The world's first large-scale, mono-digestion plant for straw is operational since 2014. The temporal and spatial biomass availability is a key issue when replicating this concept. No detailed calculations on this subject are available, and the strategic relevance of biomethane from straw in the transport sector cannot be sufficiently evaluated.Methods: To assess the balance of straw supply and use, a total of 30 data sets are combined, taking into account the cultivation of the five most important cereal types and the straw required for ten animal species, two special crops and twelve industrial uses. The data are managed at district level and presented for the years 2010 to 2018. In combination with high-resolution geodata, the results are linked to actual arable fields, and the availability of straw throughout the country is evaluated using a GIS.Results: During the analysis period, the mobilisable potential for future biomethane production is between 13.9–21.5 Tg fm a-1; this is up to 62 % higher than the previously known level. The annual potential fluctuates considerably due to weather anomalies. The all-time maximum in 2014 and the minimum for the last 26 years in 2018 are separated by just four years and a difference of 7.6 Tg fm. However, large parts of the potential are concentrated only in a few regions and liquefied biomethane could fully cover the fuel required for vessels, and up to a quarter of that for heavy goods vehicles. Up to 11.3 Tg CO2-eq. could be saved, reducing the difference to achieve the UN climate target by 3.7 %.Conclusion: Despite the strong fluctuations, the potential is sufficient to supply numerous plants and to produce relevant quantities of liquefied biomethane even in weak years. To unlock the potential, the outcomes should be discussed further with stakeholders in the identified priority regions.
Nomograms Predict Overall Survival And Cancer-Speciﬁc Survival In Patients With Fibrosarcoma: A SEER-Based Study
Authors: Xiang Guangheng , Zhu Juan-Juan , Ke Chen-Rong , Weng Yi-Min , Fang Ming-Qiao , Zhu Si-Pin , Li Yu-An , Xiao Jian , Xu Lei 
Published: March 2020

Abstract
Background Due to the rarity, it is difficult to predict the survival of patients with fibrosarcoma. This study aimed to apply a nomogram to predict survival outcomes in patients with fibrosarcoma. Methods A total of 2235 patients with diagnoses of fibrosarcoma were registered in the Surveillance, Epidemiology, and End Results database, of whom 663 patients were eventually enrolled. Univariate and multivariate Cox analyses were used to identify independent prognostic factors. Nomograms were constructed to predict 3‐ and 5‐year overall survival and cancer‐specific survival of patients with fibrosarcoma. Results In univariate and multivariate analyses of OS, age, sex, race, tumor stage, pathologic grade, use of surgery and tumor size identiﬁed as independent prognostic factors. Age, sex, tumor stage, pathologic grade, use of surgery and tumor size were significantly associated with CSS. These characteristics were further included to establish the nomogram for predicting 3- and 5- year OS and CSS. For the internal validation of the nomogram predictions of OS and CSS, the C-indices were 0.784 and 0.801. Conclusion We developed and validated the nomograms that estimated 3- and 5-year OS and CSS. These nomograms not only have good discrimination performance and calibration, but also provide patients with better clinical benefits.
Primary tumor location affects recurrence-free survival for patients with colorectal liver metastases after hepatectomy: A propensity score matched analysis
Authors: Zhang Yuanping , Wang Yongjin , Yuan Yichuan , Qiu Jiliang , Qiu Yuxiong , He Wei , Zheng Yun , Wang Zhiqiang , Gu Yangkui , Lu Zhenhai , Chen Gong , Ding Peirong , Wu Xiaojun , Pan Zhizhong , Wan Desen , Li Yuhong , Xu Ruihua , Yuan Yunfei , Li Binkui 
Published: March 2020

Abstract
Background Whether primary tumor location of colorectal cancer (CRC) affects survival of patients after resection of liver metastases remains controversial. This study was conducted to investigate the differences in clinicopathological characteristics and prognosis between right-sided CRC and left-sided CRC patients with liver metastases after hepatectomy. Methods From 2002 to 2018, 611 patients with colorectal liver metastases (CRLM) who underwent hepatectomy at our center were reviewed. Primary tumors located from cecum to transverse colon were defined as right-sided group (n = 141); tumors located from splenic flexure to rectum were defined as left-sided group (n = 470). Patients were compared between two groups before and after a 1:1 propensity score analysis (PSM). Results Before PSM, median survival time and 5-year overall survival (OS) rate in right-sided group were 77 months and 56.3%, and those in left-sided group were 64 months and 51.1%, respectively. After PSM, median survival time and 5-year OS rate in right-sided group were 77 months and 55.9%, and those in left-sided group were 58.8 months and 47.3%, respectively. The OS rates did not differ between two groups before and after PSM ( P = 0.575; P = 0.453). However, significant different recurrence free survival (RFS) rate was found before and after PSM between right-sided and left-sided group ( P = 0.028, P = 0.003). Conclusions Primary tumor location of CRC impacts RFS for patients with liver metastases after resection. A more frequent follow up to detect early recurrence might be justified for CRLM patients with a right-sided CRC.
Systemic treatment with human amnion epithelial cells after experimental traumatic brain injury
Authors: Kim Hyun Ah , Semple Bridgette D , Dill Larissa K , Pham Louise , Dworkin Sebastian , Zhang Shenpeng R , Lim Rebecca , Sobey Christopher G , McDonald Stuart J 
Published: March 2020

Abstract
Background: Systemic administration of human amnion epithelial cells (hAECs) was recently shown to reduce neuropathology and improve functional recovery following ischemic stroke in both mice and marmosets. Given the significant neuropathological overlap between ischemic stroke and traumatic brain injury (TBI), we hypothesized that a similar hAEC treatment regime would also improve TBI outcomes. Methods: Male mice (12 weeks old, n=40) were given a sham injury or moderate severity TBI by controlled cortical impact. At 60 minutes post-injury, mice were given a single tail vein injection of either saline (vehicle) or 1x10 6 hAECs suspended in saline. At 24 h post-injury, mice were assessed for locomotion and anxiety using an open field, and sensorimotor ability using a rotarod. At 48 h post-injury, brains were collected for analysis of immune cells via flow cytometry, or histological evaluation of lesion volume and hAEC penetration. To assess the impact of TBI and hAECs on lymphoid organs, spleen and thymus weights were determined. Results: Treatment with hAECs did not prevent TBI-induced sensorimotor deficits at 24 h post-injury. hAECs were detected in the injured brain parenchyma; however, lesion volume was not altered by hAEC treatment. Robust increases in several leukocyte populations in the ipsilateral hemisphere of TBI mice were found when compared to sham mice at 48 h post-injury; however, hAEC treatment did not alter brain immune cell numbers. Both TBI and hAEC treatment were found to increase spleen weight. Conclusions: Taken together, these findings indicate that — unlike in ischemic stroke — treatment with hAEC was unable to prevent immune cell infiltration and sensorimotor deficits in the acute stages following controlled cortical impact in mice. Although further investigations are required, our data suggests that the lack of hAEC-induced neuroprotection in the current study may be explained by the differential splenic contributions to neuropathology between these brain injury models.
MAGE-A4, NY-ESO-1 and SAGE expression rates and co-expression relationships in solid tumours
Authors: Ishihara Mikiya , Kageyama Shinichi , Miyahara Yoshihiro , Ishikawa Takeshi , Ueda Shugo , Soga Norihito , Naota Hiroaki , Mukai Katsumi , Harada Naozumi , Ikeda Hiroaki , Shiku Hiroshi 
Published: March 2020

Abstract
Background

Cancer testis (CT) antigens are promising targets for cancer immunotherapies such as cancer vaccines and genetically modified adoptive T cell therapy. In this study, we evaluated the expression of three CT antigens, melanoma-associated antigen A4 (MAGE-A4), New York oesophageal squamous cell carcinoma 1 (NY-ESO-1) and sarcoma antigen gene (SAGE).

Methods

MAGE-A4, NY-ESO-1 and/or SAGE antigen expression in tumour samples was evaluated by quantitative real-time polymerase chain reaction (qRT-PCR). Informed consent was obtained from individuals prior to study enrolment.

Results

In total, 585 samples in 21 tumour types were evaluated between June 2009 and March 2018. The positive expression rates of these CT antigens were as follows: MAGE-A4, 34.6% (range, 30.7-38.7); NY-ESO-1, 21.0% (range, 17.2-25.1); and SAGE, 21.8% (range, 18.5-25.4). The MAGE-A4 antigen was expressed in 54.9% of oesophageal cancers, 37.5% of head and neck cancers, 35.0% of gastric cancers and 34.2% of ovarian cancers; the NY-ESO-1 antigen was expressed in 28.6% of lung cancers, 25.3% of oesophageal cancers and 22.6% of ovarian cancers; and the SAGE antigen was expressed in 35.3% of prostate cancers, 32.9% of oesophageal cancers and 26.3% of ovarian cancers. The most common tumour type was oesophageal cancer in this study. MAGE-A4, NY-ESO-1 and SAGE antigen expression were assessed in 214 oesophageal cancer samples, among which 24 (11.2%) were triple-positive, 58 (27.1%) were positive for any two, 59 (27.6%) were positive for any one, and 73 (34.1%) were triple-negative.

Conclusions

Oesophageal cancer exhibited a relatively high rate of CT antigen positivity. Our data indicate that oesophageal cancer is a promising candidate tumour for CT antigen-targeting immunotherapy and immune monitoring.
Identification of a novel methylation gene sites signature to predict prognosis in kidney renal papillary cell carcinoma by comprehensive profiling
Authors: wang yinglei , Zhang YingYing 
Published: March 2020

Abstract
Most kidney renal papillary cell carcinoma (KIRP) patients are diagnosed at the advanced stage and have a poor prognosis. DNA methylation plays an important role in prognosis prediction of cancers. Identification of novel DNA methylation site biomarkers could be beneficial for the prognosis of KIRP patients. In this study, we aimed to find an efficient methylated sites model for predicting survival in KIRP.
The safety and effectiveness of MIDLF during one surgeon’s initial phase: accuracy, clinical outcome, complications and learning curve
Authors: Ding Hongtao , Hai Yong , Liu Yuzeng , Guan Li , Pan Aixing , Han Bo 
Published: March 2020

Abstract
ObjectiveTo characterize the safety and effectiveness during one surgeon’s initial phases of performing a Midline lumbar fusion by freehand technique based on perioperative parameters.MethodsThe first 90 consecutive patients underwent single level MIDLF, utilized a consistent technique, performed by one surgeon were retrospectively studied. A piecewise regression analysis was performed to evaluate the operation duration based on case number, and to estimate the breakpoint. The early learning period and the late steady phase was divided according to the case number of the breakpoint. Perioperative parameters and clinical data of 2 groups were compared then to elucidate if improvement in operative duration was accompanied by better patient prognosis.ResultsThe inflectional asymptote of the surgeon’s learning curve for MIDLF was achieved at the 40th case. The demographics parameters were similar between the early group of 40 patients and the latter 50. Average surgical time, intraoperative blood loss, length of incision, duration of drainage, postoperative drainage and post-operative hospitalization were significantly less in the late cohort (p<.05). Medial cortical breach was observed in 6/360 cases (4 vs. 2, P>.05), and lateral cortical breach was observed in 35/360 cases (24 vs.11, P<.05). One case of cerebrospinal fluid (CSF) leak, two cases of durotomy and one case of nerve root injury related to the technique was found in the early group, and only one case of durotomy was found in the late group. Post-surgical wound infection was seen in 2.22% (N = 2/90) of patients (2 vs. 0, P>.05). The overall complication incidence decreased alone with the learning curve, and statistical difference was achieved. Furthermore, there was no difference in clinical improvement between the two groups.ConclusionsOur result indicated that technical proficiency in MIDLF was achieved after 40 surgeries. And it is effective to significantly improve the patients’ functional status and relief the pain during one surgeon’s learning process of MIDLF in the treatment of lumbar degenerative disease, even in the initial phase. As the surgeon gains surgical proficiency and familiarity with MIDLF procedure, potential complications could be minimized. Furthermore, our results provided evidence to the excellent performance as an alternative option to traditional pedicle screw fixation.