bluuebunny/crossref_metadata_2025_split huggingface dataset:
Afirma Genomic Sequencing Classifier and Xpression Atlas Molecular Findings in Consecutive Bethesda III-VI Thyroid Nodules
Authors: Hu Mimi I , Waguespack Steven G , Dosiou Chrysoula , Ladenson Paul W , Livhits Masha J , Wirth Lori J , Sadow Peter M , Krane Jeffrey F , Stack Brendan C , Zafereo Mark E , Ali Syed Z , Weitzman Steven P , Hao Yangyang , Babiarz Joshua E , Kennedy Giulia C , Kloos Richard T 
Published: May 2021

Abstract

Context
Broad genomic analyses among thyroid histologies have been described from relatively small cohorts.

Objective
Investigate the molecular findings across a large, real-world cohort of thyroid fine-needle aspiration (FNA) samples.

Design
Retrospective analysis of RNA sequencing data files.

Setting
Clinical Laboratory Improvement Amendments laboratory performing Afirma Genomic Sequencing Classifier (GSC) and Xpression Atlas (XA) testing.

Participants
A total of 50 644 consecutive Bethesda III-VI nodules.

Intervention
None.

Main Outcome Measures
Molecular test results.

Results
Of 48 952 Bethesda III/IV FNAs studied, 66% were benign by Afirma GSC. The prevalence of BRAF V600E was 2% among all Bethesda III/IV FNAs and 76% among Bethesda VI FNAs. Fusions involving NTRK, RET, BRAF, and ALK were most prevalent in Bethesda V (10%), and 130 different gene partners were identified. Among small consecutive Bethesda III/IV sample cohorts with one of these fusions and available surgical pathology excision data, the positive predictive value of an NTRK or RET fusion for carcinoma or noninvasive follicular thyroid neoplasm with papillary-like nuclear features was &gt;95%, whereas for BRAF and ALK fusions it was 81% and 67%, respectively. At least 1 genomic alteration was identified by the expanded Afirma XA panel in 70% of medullary thyroid carcinoma classifier–positive FNAs, 44% of Bethesda III or IV Afirma GSC suspicious FNAs, 64% of Bethesda V FNAs, and 87% of Bethesda VI FNAs.

Conclusions
This large study demonstrates that almost one-half of Bethesda III/IV Afirma GSC suspicious and most Bethesda V/VI nodules had at least 1 genomic variant or fusion identified, which may optimize personalized treatment decisions.
Time-Series Analysis of Continuous Glucose Monitoring Data to Predict Treatment Efficacy in Patients with T2DM
Authors: Li Li , Sun Jie , Ruan Liemin , Song Qifa 
Published: May 2021

Abstract

Context
There is a challenge to predict treatment effects in patients with type 2 diabetes mellitus (T2DM).

Objective
To assess and predict treatment effects in patients with T2DM through time-series analysis of continuous glucose monitoring (CGM) measurements.

Method
We extracted and clustered the trend components of CGM measurements to generate representative time-series profiles, which were used as a predictor of treatment effects in groups of patients.

Setting and Participants
We recruited 111 outpatients with T2DM at Ningbo City First Hospital, China.

Intervention
The patients underwent CGM measurement for 14 days at the beginning of glucose-lowering treatment.

Main Outcome Measures
Hemoglobin A1c (HbA1c) and fasting plasma glucose (FPG) were obtained at the beginning and after 6 months of treatment.

Results
111 patients each had 960 to 1344 CGM measurements for 14 days at 96 measurements per day. The patients were classified into 3 groups according to the profiles of trend components of CGM observed values by time-series clustering method, including decreasing (47 patients), increasing (26 patients), and unchanged (38 patients) profiles. After 6 months of glucose-lowering treatment, FPG declined from 10.2 to 6.8 mmol/L (a decline of 3.4 mmol/L) in the decreasing group, from 8.9 to 9.2 mmol/L (a rise of 0.3 mmol/L) in the increasing group, and from 8.4 to 7.5 mmol/L (a decline of 0.9 mmol/L) in the unchanged group. The changes of HbA1c were 2.3%, 0.2%, and 0.9% for the 3 groups (P &lt; 0.01), respectively.

Conclusions
Clustering of the trend components of CGM data generates representative CGM profiles that are predictive of 6-month therapeutic effects for T2DM.
Osteogenesis Imperfecta: Mechanisms and Signaling Pathways Connecting Classical and Rare OI Types
Authors: Jovanovic Milena , Guterman-Ram Gali , Marini Joan C 
Published: May 2021

AbstractOsteogenesis imperfecta (OI) is a phenotypically and genetically heterogeneous skeletal dysplasia characterized by bone fragility, growth deficiency, and skeletal deformity. Previously known to be caused by defects in type I collagen, the major protein of extracellular matrix, it is now also understood to be a collagen-related disorder caused by defects in collagen folding, posttranslational modification and processing, bone mineralization, and osteoblast differentiation, with inheritance of OI types spanning autosomal dominant and recessive as well as X-linked recessive. This review provides the latest updates on OI, encompassing both classical OI and rare forms, their mechanism, and the signaling pathways involved in their pathophysiology. There is a special emphasis on mutations in type I procollagen C-propeptide structure and processing, the later causing OI with strikingly high bone mass. Types V and VI OI, while notably different, are shown to be interrelated by the interferon-induced transmembrane protein 5 p.S40L mutation that reveals the connection between the bone-restricted interferon-induced transmembrane protein-like protein and pigment epithelium-derived factor pathways. The function of regulated intramembrane proteolysis has been extended beyond cholesterol metabolism to bone formation by defects in regulated membrane proteolysis components site-2 protease and old astrocyte specifically induced-substance. Several recently proposed candidate genes for new types of OI are also presented. Discoveries of new OI genes add complexity to already-challenging OI management; current and potential approaches are summarized.
Data extraction methods for systematic review (semi)automation: A living systematic review
Authors: Schmidt Lena , Olorisade Babatunde K. , McGuinness Luke A. , Thomas James , Higgins Julian P. T. 
Published: May 2021

Background: The reliable and usable (semi)automation of data extraction can support the field of systematic review by reducing the workload required to gather information about the conduct and results of the included studies. This living systematic review examines published approaches for data extraction from reports of clinical studies. Methods: We systematically and continually search MEDLINE, Institute of Electrical and Electronics Engineers (IEEE), arXiv, and the dblp computer science bibliography databases. Full text screening and data extraction are conducted within an open-source living systematic review application created for the purpose of this review. This iteration of the living review includes publications up to a cut-off date of 22 April 2020. Results: In total, 53 publications are included in this version of our review. Of these, 41 (77%) of the publications addressed extraction of data from abstracts, while 14 (26%) used full texts. A total of 48 (90%) publications developed and evaluated classifiers that used randomised controlled trials as the main target texts. Over 30 entities were extracted, with PICOs (population, intervention, comparator, outcome) being the most frequently extracted. A description of their datasets was provided by 49 publications (94%), but only seven (13%) made the data publicly available. Code was made available by 10 (19%) publications, and five (9%) implemented publicly available tools. Conclusions: This living systematic review presents an overview of (semi)automated data-extraction literature of interest to different types of systematic review. We identified a broad evidence base of publications describing data extraction for interventional reviews and a small number of publications extracting epidemiological or diagnostic accuracy data. The lack of publicly available gold-standard data for evaluation, and lack of application thereof, makes it difficult to draw conclusions on which is the best-performing system for each data extraction target. With this living review we aim to review the literature continually.
Tunable laser operation of Tm3+:KY3F10 near 1.9  µm via upconversion pumping at 1064  nm
Authors: Morova Yagız , Kamun Eylul Nıhan , Tonelli Mauro , Sennaroglu Alphan 
Published: May 2021

We experimentally demonstrate, for the first time to our knowledge, that upconversion pumping can be employed with a 1064-nm fiber laser to achieve tunable laser operation with 8 at. %

T

m

3
+

:

K
Y

3

F

10

crystal near 1.9 µm, in addition to the previously explored upconversion pumping of the 2.3-µm laser transition. Two different sets of cavity optics were used to investigate lasing at 1.9 and 2.3 µm, corresponding to the laser transitions

3

F

4

−

3

H

6

and

3

H

4

−

3

H

5

, respectively. In the case of the

3

F

4

−

3

H

6

laser transition, an x-cavity laser oscillator was constructed with a 2.3% output coupler and as high as 142 mW of output power was obtained at an incident pump power of 1.9 W at 1064 nm. Tunable laser operation could be obtained between 1849 and 1994 nm by using

C
a

F

2

and suprasil prisms. The highest slope efficiency of 29% with respect to average absorbed pump power was obtained with a 5.5% output coupler. For the case of 1.9 µm lasing, it was further demonstrated that the nonlinear absorption of the crystal at 1064 nm depends on the intracavity laser intensity as well as the pump intensity. The

3

H

4

−

3

H

5

laser transition was also investigated with the same crystal in a z-cavity configuration under upconversion pumping, giving as high as 130 mW of output power at the central wavelength of 2344 nm with 1.6 W of incident pump power.
MiRNA-107 enhances the malignant progression of pancreatic cancer by targeting TGFBR3
Authors: Tian Tingke , Yang Quanzhong , Zhang Cuijuan , Li Xiaokun , Cheng Jiancheng 
Published: May 2021

Background
The prognosis of pancreatic cancer (PC) is relatively dismal due to the lack of effective therapy. In this study, we explored the specific functions and molecular mechanisms of miR-107 to uncover effective therapeutic targets for PC.

Method
The miR-107 expression in PC cell lines was assessed via quantitative real-time polymerase chain reaction (qRT-PCR). Besides, online bioinformatics analysis was adopted to predict the underlying targets of miR-107. Meanwhile, TCGA database was employed to explore the prognosis of PC patients. In addition, MTT and transwell assays were conducted to explore the PC cells’ biological functions.

Result
MiR-107 was remarkably increased in PC cells which could promote the proliferation, invasion and migration of PC cells. In addition, miR-107 could directly down-regulate TGFBR3 expression through binding to TGFBR3 3’UTR. Survival analysis from TCGA suggested that PC patients with higher miR-107 expression was significantly involved in poorer prognosis.

Conclusion
We concluded that miR-107 promoted proliferation, invasion and migration of PC cells via targeting TGFBR3, which may provide novel underlying therapeutic targets.
Health system interventions to integrate genetic testing in routine oncology services: A systematic review
Authors: O’Shea Rosie , Taylor Natalie , Crook Ashley , Jacobs Chris , Jung Kang Yoon , Lewis Sarah , Rankin Nicole M. 
Published: May 2021

Background
Integration of genetic testing into routine oncology care could improve access to testing. This systematic review investigated interventions and the tailored implementation strategies aimed at increasing access to genetic counselling and testing and identifying hereditary cancer in oncology.

Methods
The search strategy results were reported using the PRISMA statement and four electronic databases were searched. Eligible studies included routine genetic testing for breast and ovarian cancer or uptake after universal tumour screening for colorectal or endometrial cancer. The titles and abstracts were reviewed and the full text articles screened for eligibility. Data extraction was preformed using a designed template and study appraisal was assessed using an adapted Newcastle Ottawa Scale. Extracted data were mapped to Proctor’s et al outcomes and the Consolidated Framework for Implementation Research and qualitatively synthesised.

Results
Twenty-seven studies, published up to May 2020, met the inclusion criteria. Twenty-five studies ranged from poor (72%), fair to good (28%) quality. Most interventions identified were complex (multiple components) such as; patient or health professional education, interdisciplinary practice and a documentation or system change. Forty-eight percent of studies with complex interventions demonstrated on average a 35% increase in access to genetic counselling and a 15% increase in testing completion.
Mapping of study outcomes showed that 70% and 32% of the studies aligned with either the service and client or the implementation level outcome and 96% to the process or inner setting domains of the Consolidated Framework for Implementation Research.

Conclusion
Existing evidence suggests that complex interventions have a potentially positive effect towards genetic counselling and testing completion rates in oncology services. Studies of sound methodological quality that explore a greater breadth of pre and post implementation outcomes and informed by theory are needed. Such research could inform future service delivery models for the integration of genetics into oncology services.
Preserved intention understanding during moral judgments in schizophrenia
Authors: Kronbichler Lisa , Stelzig-Schöler Renate , Lenger Melanie , Weber Stefanie , Pearce Brandy-Gale , Reich Luise-Antonia , Aichhorn Wolfgang , Kronbichler Martin 
Published: May 2021

Introduction
Although there is convincing evidence for socio-cognitive impairments in schizophrenia spectrum disorder (SSD), little evidence is found for deficient moral cognition. We investigated whether patients with SSD showed altered moral judgments in a story task where the protagonist either had a neutral or malicious intention towards another person. This paradigm examined whether SSD relates to altered moral cognition in general or specifically to impaired integration of prior information (such as beliefs) in moral judgments.

Methods
23 patients and 32 healthy controls read vignettes created in a 2 x 2 design. The protagonist in each story either had a neutral or negative intention towards another person which, as a result, either died (negative outcome) or did not die (neutral outcome). Participants rated the moral permissibility of the protagonist’s action. Standard null hypothesis significance testing and equivalent Bayes analyses are reported.

Results
Schizophrenia patients did not differ significantly in permissibility ratings from healthy controls. This finding was supported by the Bayes analyses which favoured the null hypothesis. Task performance was not related to symptom severity or medication.

Conclusions
The current findings do not support the notion that moral judgments are deficient in schizophrenia. Furthermore, the current study shows that patients do not have observable difficulties in integrating the protagonist’s belief in the rating of the moral permissibility of the action-outcome.
Acetaldehyde breath test as a cancer risk marker in patients with esophageal and hypopharyngeal squamous cell carcinoma
Authors: Sasaki Fumisato , Kanmura Shuji , Oda Kohei , Maeda Hidehito , Kabayama Masayuki , Iwaya Hiromichi , Komaki Yuga , Arima Shiho , Tanoue Shiroh , Hashimoto Shinichi , Fujita Hiroshi , Ido Akio 
Published: May 2021

Patients with inactive acetaldehyde dehydrogenase 2 (ALDH2) are at high risk for esophageal squamous cell carcinoma (ESCC) and hypopharyngeal squamous cell carcinoma (HPSCC). The acetaldehyde breath test (ABT) may demonstrate ALDH2 gene polymorphisms. We evaluated the usefulness of the ABT in patients with ESCC and HPSCC. The squamous cell carcinoma (SCC) group consisted of 100 patients who were treated with endoscopic submucosal dissection (ESD) for ESCC or HPSCC, and the control group (HC) consisted of 275 healthy subjects. The SCC group comprised the “single subgroup” (n = 63), in which a single lesion was initially treated with ESD, and the “multiple subgroup” (n = 31), in which multiple lesions were initially treated with ESD. First, we compared the groups’ risk factors for carcinogenesis and measured the acetaldehyde-to-ethanol (A/E) ratio. Then we tested the groups’ differences in the abovementioned carcinogenic risk factors. We found that the proportion of individuals in the SCC group with inactive ALDH2 (A/E ratio ≥ 23.3) was significantly higher than that in the HC group (p = 0.035), as was the A/E ratio (p < 0.001). Also, the proportion of individuals with inactive ALDH2 in the multiple subgroup was significantly higher than that in single subgroup (p = 0.015), as was the A/E ratio (p = 0.008). In conclusion, ABT may be a potential screening tool for detecting people at risk of ESCC and HPSCC. In addition, it could be a useful tool in detecting patients at risk of multiple or double carcinomas among patients with ESCC and HPSCC.
Trial registration: Trial Registration number: UMIN000040615 [https://rctportal.niph.go.jp/en/detail?trial_id=UMIN000040615], Data of Registration: 01 46 June 2020, retrospectively registered.
Statistical modeling of numbers of human deaths per road traffic accident in the Oromia region, Ethiopia
Authors: Aga Merga Abdissa , Woldeamanuel Berhanu Teshome , Tadesse Mekonnen 
Published: May 2021

Background
Globally, road traffic accidents are the leading causes of death among young people in general, and the main cause of death among young people aged 15–29 years. Recently, in Ethiopia, the number of road traffic accidents has been increasing. The study aimed to identify the potential factors associated with the number of human deaths by road traffic accidents in the Oromia Regional State, Ethiopia.

Methods
We used data obtained from the Oromia region traffic police office recorded on daily basis road traffic accidents from July 2016 up to July 2017. Count regression models were was used to analyses the factors associated with the number of human deaths from road traffic accidents.

Results
Age of the driver’s 31–50 years (AOR = 0.289, 95%CI: 0.175, 0.479) and higher than 50 years old (AOR = 0.311, 95%CI: 0.129, 0.751), driver’s years of experience 5–10 years (AOR = 0.014, 95%CI: 0.007, 0.027), and more than 10 years (AOR = 0.101, 95%CI: 0.057, 0.176), automobile vehicle type (AOR = 8.642, 95%CI: 2.7644, 27.023), vehicle years of service 5–10 years (AOR = 2.484, 95%CI: 1.194, 5.169), and more than 10 years (AOR = 2.639, 95%CI: 1.268, 5.497), vehicle upside down accidents (AOR = 5.560, 95%CI: 2.506, 12.336), turning illegal position (AOR = 0.454, 95%CI: 0.226, 0.913), residential areas (AOR = 108.506, 95%CI: 13.725, 857.798), and working areas (AOR = 129.606, 95%CI: 16.448, 1021.263) were significant associated number of human deaths per road traffic accident factors in the study area.

Conclusion
Human deaths per road traffic accidents occurred due to the younger age of the driver, driver’s lack of sufficient experience, vehicle serviced for long years, driving on a wet road, driving in the afternoon, driving near/around residential places and vehicle to driver’s relation. Thus, the regional traffic police should give special attention to younger drivers, less experienced drivers, old vehicles, driving near residential areas, driving automobiles, and driving in the afternoon to control traffic system to reduce the number of human deaths pear road traffic accident.
Assessment of in vivo bone microarchitecture changes in an anti-TNFα treated psoriatic arthritic patient
Authors: Soldati Enrico , Escoffier Lucas , Gabriel Sophie , Ogier Augustin C. , Chagnaud Christophe , Mattei Jean P. , Cammilleri Serge , Bendahan David , Guis Sandrine 
Published: May 2021

Objective
Psoriatic arthritis (PsA) is an inflammatory rheumatic disease, mediated in part by TNFα and associated with bone loss. Anti-TNFα treatment should inhibit this phenomenon and reduce the systemic bone loss. Ultra-high field MRI (UHF MRI) may be used to quantify bone microarchitecture (BM) in-vivo. In this study, we quantified BM using UHF MRI in a PsA patient and followed up the changes related to anti-TNFα treatment.

Subjects and methods
A non-treated PsA patient with knee arthritis and 7 gender-matched controls were scanned using a gradient re-echo sequence at UHF MRI. After a year of Adalimumab treatment, the patient underwent a second UHF MRI. A PET-FNa imaging was performed before and after treatment to identify and localize the abnormal metabolic areas. BM was characterized using typical morphological parameters quantified in 32 regions of interest (ROIs) located in the patella, proximal tibia, and distal femur.

Results
Before treatment, the BM parameters were statistically different from controls in 24/32 ROIs with differences reaching up to 38%. After treatment, BM parameters were normalized for 15 out of 24 ROIs. The hypermetabolic areas disclosed by PET-FNa before the treatment partly resumed after the treatment.

Conclusion
Thanks to UHF MRI, we quantified in vivo BM anomalies in a PsA patient and we illustrated a major reversion after one year of treatment. Moreover, BM results highlighted that the abnormalities were not only localized in hypermetabolic regions identified by PET-FNa, suggesting that the bone loss was global and not related to inflammation.
Parkinson’s disease case ascertainment in a large prospective cohort
Authors: Shrestha Srishti , Parks Christine G. , Richards-Barber Marie , Chen Honglei , Sandler Dale P. 
Published: May 2021

Background
In epidemiologic studies where physician-based case adjudication is not feasible, Parkinson’s disease (PD) case ascertainment is often limited to self-reports which may not be accurate. We evaluated strategies to identify PD cases in the Agricultural Health Study (AHS).

Methods
Doctor-diagnosed PD was self-reported on all cohort-wide surveys; potential cases were also identified from death certificates. Follow-up surveys asked about PD-related motor and non-motor symptoms. For PD confirmation, we collected additional diagnosis, symptom, and treatment data from 510 potential PD cases or their proxy (65% of those contacted) in a supplemental screener and obtained medical records for a subset (n = 65). We classified PD cases using established criteria and screener data.

Results
Of 510 potential PD cases, 75% were considered “probable” or “possible”; this proportion increased among participants diagnosed by a specialist (81.2%), taking PD medication (85.2%), or reporting ≥5 motor symptoms (86.8%) in a regular AHS survey. Of those with medical records, 93% (57 of 61) of probable or possible PD was confirmed. Never-smoking and non-motor and motor symptoms reported in prior AHS surveys were more common with probable/possible PD than unconfirmed PD.

Conclusion
In this retrospective PD case ascertainment effort, we found that PD self-report with information on motor symptoms or medications may be a reasonable alternative for identifying PD cases when physician exam is not feasible. Because of intervening mortality, screeners could not be obtained from about one-third of those contacted. Thus, findings warrant replication.