bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reporting on the level of validity and reliability of questionnaires measuring Katakori severity: A systematic review
Authors: Aoki Kaori , Hall Toby , Takasaki Hiroshi 
Published: March 2019

Objectives: Katakori is a Japanese term for non-specific symptoms including discomfort or dull pain caused by muscle stiffness around the neck through the shoulders and is one of the most frequently reported symptoms in Japan. However, there has been no standardized patient-reported outcome measure to evaluate Katakori severity. This study aimed to investigate the reporting level on validity and reliability of patient-reported outcome measures of Katakori severity. Method: A systematic search in ICHUSHI, MEDLINE, EMBASE and PubMed was undertaken from inception to April 2017 without language limitations. Two authors independently undertook screening by inspecting the title and abstract. Inclusion criteria were as follows: (1) participants with Katakori symptoms, (2) reporting reliability or validity of questionnaire evaluating Katakori severity and (3) published journal articles. Studies that either of the authors retained through the screening process were inspected with full text by the two authors independently to examine eligibility of the study. Any disagreement on eligibility after full-text inspection was resolved by discussion between them. Methodological quality was rated with the COnsensus-based Standards for the selection of health Measurement INstruments checklist. Subsequently, the evidence level of each measurement property was assessed for each questionnaire. The two authors extracted data independently. Any disagreement was resolved by discussion between them. Results: Five questionnaires were identified in five studies. The Shoulder Pain and Disability Index and Scale for Measuring Felt Shoulder Stiffness had the highest level of methodological quality. However, excellent measurement properties were found in only two out of nine criteria. Furthermore, in particular, content validity was not investigated in any measure. Conclusion: There is preliminary evidence for the reliability and validity of the Shoulder Pain and Disability Index and Scale for Measuring Felt Shoulder Stiffness; however, much further research is required. Identifying or developing a patient-reported outcome measure with content validity would be a future research agenda.
Delta neutrophil index as an early predictive marker of severe acute pancreatitis in the emergency department
Authors: Kim Tae Y , Kim Sun J , Kim Yoon S , Lee Jong W , Park Eung J , Lee Seok J , Lee Kyong J , Cha Yong S 
Published: March 2019

BackgroundPredicting severe acute pancreatitis (AP) in the early clinical stage is important for low morbidity and mortality. Delta neutrophil index (DNI) is used to detect infection and inflammation, but no previous studies have evaluated the usefulness of DNI as an early predictor of progression to severe AP (SAP).MethodsThe medical records of patients who were diagnosed with AP at the emergency department (ED) of Wonju Severance Christian Hospital from January 2012 to August 2016 were retrospectively reviewed. The initial DNI obtained in the ED was compared with other inflammatory markers to predict SAP. Multivariate logistic regression was used for statistical analysis.ResultsOf the 209 cases included in the analysis, 13 were classified as SAP. Compared to the DNI of the mild to moderately SAP group, that in the SAP group was considerably higher. The DNI showed a positive correlation with the Atlanta classification and bedside index of severity in AP. Using multivariate logistic regression analysis, DNI was an independent predictor of early SAP detection (odds ratio 1.122, 95% CI 1.045–1.205, p = 0.001). Among the biomarkers, DNI had the highest predictive value for SAP.ConclusionsThe DNI measured in the ED at presentation is a potentially useful adjunctive marker to predict SAP.
A new breast tomosynthesis imaging method: Continuous Sync-and-Shoot – technical feasibility and initial experience
Authors: Jousi Mikko O , Erkkilä Jukka , Varjonen Mari , Soiva Martti , Hukkinen Katja , Blanco Sequeiros Roberto 
Published: March 2019

Background Digital breast tomosynthesis (DBT) is gaining popularity in breast imaging. There are several different technical approaches for conducting DBT imaging. Purpose To determine optimal imaging parameters, test patient friendliness, evaluate the initial diagnostic performance, and describe diagnostic advances possible with the new Continuous Sync-and-Shoot method. Material and Methods Thirty-six surgical breast specimens were imaged with digital mammography (DM) and a prototype of a DBT system (Planmed Oy, Helsinki, Finland). We tested the patient friendliness of the sync-and-shoot movement without radiation exposure in eight volunteers. Different imaging parameters were tested with 20 specimens to identify the optimal combination: angular range 30°, 40°, and 60°; pixel binning; Rhodium (Rh) and Silver (Ag) filtrations; and different kV and mAs values. Two breast radiologists evaluated 16 DM and DBT image pairs and rated six different image properties. Imaging modalities were compared with paired t-test. Results The Continuous Sync-and-Shoot method produced diagnostically valid images. Five out of eight volunteers felt no/minimal discomfort, three experienced mild discomfort from the tilting movement of the detector, with the motion being barely recognized. The combination of 30°, Ag filtering, and 2 × 2 pixel binning produced the best image quality at an acceptable dose level. DBT was significantly better in all six evaluated properties ( P < 0.05). Mean DoseDBT/DoseDM ratio was 1.22 (SD = 0.42). Conclusion The evaluated imaging method is feasible for imaging and analysing surgical breast specimens and DBT is significantly better than DM in image evaluation.
Geometry of Torsional Malalignment Syndrome: Trochlear Dysplasia but Not Torsion Predicts Lateral Patellar Instability
Authors: Balcarek Peter , Radebold Tobias , Schulz Xenia , Vogel Dennis 
Published: March 2019

Background: The clinical impact of increased torsion on patellar instability and patellofemoral pain syndrome (PFPS) has been suggested by several studies. Hypothesis: The hypotheses of this study were that (1) torsional malalignment (TM) is characterized by a positive correlation between different malalignment parameters that represent an overall picture of the malalignment syndrome and (2) an increase in overall torsion is the underlying difference between patellar instability and isolated patellofemoral pain. Study Design: Cohort study; Level of evidence, 3. Methods: Between April 2015 and July 2017, a total of 428 patients were treated for lateral patellar dislocation (LPD), and 333 patients were treated for PFPS. Sixty-two patients (14.5%) with patellar instability (LPD group) and 29 patients (8.7%) with patellofemoral pain (PFPS group) had additional TM and were included in this study. All patients underwent magnetic resonance imaging for torsional alignment and patellar tracking, including femoral antetorsion, tibial torsion, knee rotation, tibial tuberosity–trochlear groove (TT-TG) distance, tibial tuberosity–posterior cruciate ligament (TT-PCL) distance, Dejour classification of trochlear dysplasia, lateral trochlear inclination (LTI) angle, and patellar height. Results: The LPD and PFPS groups differed significantly in terms of trochlear dysplasia ( P < .001), LTI angle ( P < .001), and TT-TG distance ( P = .0167) but did not differ in terms of femoral antetorsion (20.02° ± 8.80° vs 20.03° ± 7.91°, respectively; P = .8545), tibial torsion (39.53° ± 9.23° vs 41.24° ± 7.28°, respectively; P = .3616), or knee rotation (10.42° ± 5.16° vs 8.48° ± 7.81°, respectively; P = .0163). Only measures of TT-TG distance and TT-PCL distance and measures of TT-TG distance and knee rotation were positively correlated. Trochlear dysplasia (type B-D) was identified as the only significant predictor of patellar instability. Conclusion: TM in patients with either PFPS or LPD does not appear to be characterized by a fixed constellation of different malalignment parameters. Between groups, the parameters differed significantly only in terms of trochlear dysplasia and the TT-TG distance, and trochlear dysplasia (type B-D) (but not torsion) was identified as a predictor of lateral patellar instability.
Diagnosis of non-neoplastic renal diseases in renal mass biopsies
Authors: Tjota Melissa Y , Gallan Alexander J , Paner Gladell P , Antic Tatjana , Shalhav Arieh L , Eggener Scott E , Henriksen Kammi J , Chang Anthony 
Published: March 2019

Purpose: As up to 25% of renal neoplasms may be benign, renal function preservation is often a priority in the management of small renal masses. Studies have demonstrated the occurrence of non-neoplastic renal diseases in nephrectomy specimens, but this has not been studied in the setting of renal mass biopsy. Therefore, we conducted this study to determine the feasibility of evaluating the non-neoplastic renal parenchyma in such a limited tissue sample. Methods: We identified 117 needle biopsies for renal lesions in adults from the Department of Pathology archives (2007–2017). Additional stains for periodic acid–Schiff or Jones methenamine silver were obtained as needed. Results: Of 117 cases, non-neoplastic renal parenchyma was absent in 91 cases (78%) and present in 26 cases (22%). Review of the hematoxylin and eosin slides identified 6 cases (5%) with significant diffuse and/or nodular mesangial sclerosis. Additional review of the periodic acid–Schiff and Jones’ stains demonstrated two cases that showed diffuse and focally nodular mesangial sclerosis that was consistent with diabetic nephropathy. Conclusions: The needle biopsy is increasingly useful in guiding the management of patients with small renal masses. Although less than 25% of renal mass biopsies had sufficient non-neoplastic renal parenchyma for pathologic evaluation, medical renal diseases, such as diabetic nephropathy, could be diagnosed. On the contrary, the biopsy specimens for urothelial lesions rarely yield sufficient adjacent non-neoplastic renal parenchyma for pathologic evaluation.
A systematic review of pharmacotherapeutic clinical trial end-points for bronchiectasis in adults
Authors: Crichton Megan L. , Aliberti Stefano , Chalmers James D. 
Published: March 2019

Bronchiectasis is an increasing clinical problem, but multiple recent clinical trials have failed to reach their primary end-point. Difficulties in achieving “positive” bronchiectasis trials is reflected in a lack of agreement from trialists and regulators on what are the optimal end-points.To evaluate the use of end-points in bronchiectasis trials, we conducted a systematic review of published bronchiectasis trials from 2008 to 2018 and extracted end-points used, definitions, methods of analysis and responsiveness.Our analysis shows that quality of life and exacerbation end-points are most frequently used. Trials using exacerbation end-points have been characterised by varying definitions, multiple methods of analysis and durations of follow-up. There are multiple quality of life tools for bronchiectasis (Quality of Life – Bronchiectasis questionnaire, St George's Respiratory Questionnaire,etc.). The majority of studies measure lung function (e.g.forced expiratory volume in 1 s), but this is shown to be nonresponsive to the majority of interventions. Microbiology end-points frequently show statistically significant differences in phase 2 antibiotic studies but their correlation with clinical end-points is unknown.This systematic review demonstrates a need for guidance to standardise definitions and design features to improve reproducibility and increase the likelihood of demonstrating statistically significant benefits with new therapies.
A k-mer grammar analysis to uncover maize regulatory architecture
Authors: Mejía-Guerra María Katherine , Buckler Edward S. 
Published: March 2019

Abstract
Background
Only a small percentage of the genome sequence is involved in regulation of gene expression, but to biochemically identify this portion is expensive and laborious. In species like maize, with diverse intergenic regions and lots of repetitive elements, this is an especially challenging problem that limits the use of the data from one line to the other. While regulatory regions are rare, they do have characteristic chromatin contexts and sequence organization (the grammar) with which they can be identified.

Results
We developed a computational framework to exploit this sequence arrangement. The models learn to classify regulatory regions based on sequence features - k-mers. To do this, we borrowed two approaches from the field of natural language processing: (1) “bag-of-words” which is commonly used for differentially weighting key words in tasks like sentiment analyses, and (2) a vector-space model using word2vec (vector-k-mers), that captures semantic and linguistic relationships between words. We built “bag-of-k-mers” and “vector-k-mers” models that distinguish between regulatory and non-regulatory regions with an average accuracy above 90%. Our “bag-of-k-mers” achieved higher overall accuracy, while the “vector-k-mers” models were more useful in highlighting key groups of sequences within the regulatory regions.

Conclusions
These models now provide powerful tools to annotate regulatory regions in other maize lines beyond the reference, at low cost and with high accuracy.
Partial-body cryostimulation after training improves sleep quality in professional soccer players
Authors: Douzi Wafa , Dupuy Olivier , Theurot Dimitri , Boucard Geoffroy , Dugué Benoit 
Published: March 2019

Abstract
Objective
The aim of the present investigation was to determine whether using cryostimulation (partial-body cryostimulation) impacts sleep quality in professional soccer players. Different exposure durations at − 180 °C were tested randomly after standardized training sessions in nine professional soccer players (no cryostimulation, 180-s exposure, two 90-s exposures separated by a 5-min rest at room temperature, and 90-s exposure), and the effects on sleep quality using 3-dimensional accelerometers worn during sleep were assessed.

Results
The number of movements during the night after partial-body cryostimulation was significantly reduced only in the 180-s exposure condition (p < 0.05, very large effect size) compared with the control condition. Partial-body cryostimulation seems to induce a positive impact on sleep quality that may be dose-dependent.
Trial registration Australia and New Zealand Clinical Trials Registry (ANZCTR), ACTRN12619000330145, date of registration: 4/03/2019. Retrospectively registered
Cell membrane protein functionalization of nanoparticles as a new tumor‐targeting strategy
Authors: Pasto Anna , Giordano Federica , Evangelopoulos Michael , Amadori Alberto , Tasciotti Ennio 
Published: March 2019

AbstractNanoparticles have seen considerable popularity as effective tools for drug delivery. However, non‐specific targeting continues to remain a challenge. Recently, biomimetic nanoparticles have emerged as an innovative solution that exploits biologically‐derived components to improve therapeutic potential. Specifically, cell membrane proteins extracted from various cells (i.e., leukocytes, erythrocytes, platelets, mesenchymal stem cells, cancer) have shown considerable promise in bestowing nanoparticles with increased circulation and targeting efficacy. Traditional nanoparticles can be detected and removed by the immune system which significantly hinders their clinical success. Biomimicry has been proposed as a promising approach to overcome these limitations. In this review, we highlight the current trends in biomimetic nanoparticles and describe how they are being used to increase their chemotherapeutic effect in cancer treatment.
The expanding repertoire of hereditary information carriers
Authors: Zhang Ying , Chen Qi 
Published: March 2019

ABSTRACT
A hereditary system that is based on double-helix DNA sequences provides a stable way to store inherited traits and is favored by most life forms on Earth. However, emerging studies on the phenomenon of non-DNA sequence-based inheritance in multiple species, including mammals, urges a rethinking of the nature of hereditary information carriers and the ways in which they encode heritable traits. In this short opinion piece, we discuss how potential hereditary information carriers such as DNA-associated proteins, epigenetic marks, RNAs and organelles could function via distinct and synergistic modes of action in encoding and transmitting ancestral traits, either inherited or acquired from the environment. In particular, we discuss how the 3D structure of chromatin, in addition to its DNA sequence, may represent a higher-order carrier of hereditary information.
DamID as a versatile tool for understanding gene regulation
Authors: Aughey Gabriel N. , Cheetham Seth W. , Southall Tony D. 
Published: March 2019

ABSTRACT
The interaction of proteins and RNA with chromatin underlies the regulation of gene expression. The ability to profile easily these interactions is fundamental for understanding chromatin biology in vivo. DNA adenine methyltransferase identification (DamID) profiles genome-wide protein-DNA interactions without antibodies, fixation or protein pull-downs. Recently, DamID has been adapted for applications beyond simple assaying of protein-DNA interactions, such as for studying RNA-chromatin interactions, chromatin accessibility and long-range chromosome interactions. Here, we provide an overview of DamID and introduce improvements to the technology, discuss their applications and compare alternative methodologies.
Nr5a1 suppression during the murine fetal period optimizes ovarian development by fine-tuning Notch signaling
Authors: Nomura Risa , Kashimada Kenichi , Suzuki Hitomi , Zhao Liang , Tsuji-Hosokawa Atsumi , Yagita Hideo , Takagi Masatoshi , Kanai Yoshiakira , Bowles Josephine , Koopman Peter , Kanai-Azuma Masami , Morio Tomohiro 
Published: March 2019

ABSTRACT
The nuclear receptor NR5A1 is equally expressed and required for development of the gonadal primordia of both sexes, but, after sex determination, it is upregulated in XY testes and downregulated in XX ovaries. We have recently demonstrated, in mice, that this downregulation is mediated by forkhead box L2 (FOXL2) and hypothesized that adequate suppression of Nr5a1 is essential for normal ovarian development. Further, analysis of human patients with disorders/differences of sex development suggests that overexpression of NR5A1 can result in XX (ovo)testicular development. Here, we tested the role of Nr5a1 by overexpression in fetal gonads using a Wt1-BAC (bacterial artificial chromosome) transgene system. Enforced Nr5a1 expression compromised ovarian development in 46,XX mice, resulting in late-onset infertility, but did not induce (ovo)testis differentiation. The phenotype was similar to that of XX mice lacking Notch signaling. The expression level of Notch2 was significantly reduced in Nr5a1 transgenic mice, and the ovarian phenotype was almost completely rescued by in utero treatment with a NOTCH2 agonist. We conclude that suppression of Nr5a1 during the fetal period optimizes ovarian development by fine-tuning Notch signaling.
An intra-population heterothermy continuum: notable repeatability of body temperature variation in food-deprived yellow-necked mice
Authors: Boratyński Jan S. , Iwińska Karolina , Bogdanowicz Wiesław 
Published: March 2019

ABSTRACT
Theoretical modelling predicts that the thermoregulatory strategies of endothermic animals range from those represented by thermal generalists to those characteristic for thermal specialists. While the generalists tolerate wide variations in body temperature (Tb), the specialists maintain Tb at a more constant level. The model has gained support from inter-specific comparisons relating to species and population levels. However, little is known about consistent among-individual variation within populations that could be shaped by natural selection. We studied the consistency of individual heterothermic responses to environmental challenges in a single population of yellow-necked mice (Apodemus flavicollis), by verifying the hypothesis that Tb variation is a repeatable trait. To induce the heterothermic response, the same individuals were repeatedly food deprived for 24 h. We measured Tb with implanted miniaturised data loggers. Before each fasting experiment, we measured basal metabolic rate (BMR). Thus, we also tested whether individual variation of heterothermy correlates with individual self-maintenance costs, and the potential benefits arising from heterothermic responses that should correlate with body size/mass. We found that some individuals clearly entered torpor while others kept Tb stable, and that there were also individuals that showed intermediate thermoregulatory patterns. Heterothermy was found to correlate negatively with body mass and slightly positively with the BMR achieved 1–2 days before fasting. Nonetheless, heterothermy was shown to be highly repeatable, irrespective of whether we controlled for self-maintenance costs and body size. Our results indicate that specialist and generalist thermoregulatory phenotypes can co-exist in a single population, creating a heterothermy continuum.
CT-based ventilation imaging in radiation oncology
Authors: Vinogradskiy Yevgeniy 
Published: March 2019

A form of lung function imaging is emerging that uses phase-resolved four-dimensional CT (4DCT or breath-hold CT) images along with image processing techniques to generate lung function maps that provide a surrogate of lung ventilation. CT-based ventilation (referred to as CT-ventilation) research has gained momentum in Radiation Oncology because many lung cancer patients undergo four-dimensional CT simulation as part of the standard treatment planning process. Therefore, generating CT-ventilation images provides functional information without burdening the patient with an extra imaging procedure. CT-ventilation has progressed from an image processing calculation methodology, to validation efforts, to retrospective demonstration of clinical utility in Radiation Oncology. In particular, CT-ventilation has been proposed for two main clinical applications: functional avoidance radiation therapy and thoracic dose–response assessment. The idea of functional avoidance radiation therapy is to preferentially spare functional portions of the lung (as measured by CT-ventilation) during radiation therapy with the hypothesis that reducing dose to functional portions of the lung will lead to reduced rates of radiation-related thoracic toxicity. The idea of imaging-based dose–response assessment is to evaluate pre- to post-treatment CT-ventilation-based imaging changes. The hypothesis is that early, imaging-change-based response can be an early predictor of subsequent thoracic toxicity. Based on the retrospective evidence, the clinical applications of CT-ventilation have progressed from the retrospective setting to on-going prospective clinical trials. This review will cover basic CT-ventilation calculation methodologies, validation efforts, presentation of clinical applications, summarize on-going clinical trials, review potential uncertainties and shortcomings of CT-ventilation, and discuss future directions of CT-ventilation research.