bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Japanese Society of Pathology Practical Guidelines on the handling of pathological tissue samples for cancer genomic medicine
Authors: Hatanaka Yutaka , Kuwata Takeshi , Morii Eiichi , Kanai Yae , Ichikawa Hitoshi , Kubo Takashi , Hatanaka Kanako C. , Sakai Kazuko , Nishio Kazuto , Fujii Satoshi , Okamoto Wataru , Yoshino Takayuki , Ochiai Atsushi , Oda Yoshinao 
Published: October 2021

AbstractClinical cancer genomic testing based on next‐generation sequencing can help select genotype‐matched therapy and provide diagnostic and prognostic information. Pathological tissue from malignant tumors obtained during routine practice are frequently used for genomic testing. This article is aimed to standardize the proper handling of pathological specimens in practice for genomic medicine based on the findings established in “Guidelines on the handling of pathological tissue samples for genomic medicine (in Japanese)” published by The Japanese Society of Pathology (JSP) in 2018. The two‐part practical guidelines are based on empirical data analyses; Part 1 describes the standard preanalytic operating procedures for tissue collection, processing, and storage of formalin‐fixed paraffin‐embedded (FFPE) samples, while Part 2 describes the assessment and selection of FFPE samples appropriate for genomic testing, typically conducted by a pathologist. The guidelines recommend that FFPE sample blocks be used within 3 years from preparation, and the tumor content should be ≥30% (minimum 20%). The empirical data were obtained from clinical studies performed by the JSP in collaboration with leading Japanese cancer genome research projects. The Japanese Ministry of Health, Labour, and Welfare (MHLW) recommended to comply with the JSP practical guidelines in implementing cancer genomic testing under the national health insurance system in over 200 MHLW‐designated core and cooperative cancer genome medicine hospitals in Japan.
Behavior‐based POI recommendation for small groups in location‐based social networks
Authors: Bahari Sojahrood Zahra , Taleai Mohammad 
Published: October 2021

AbstractIn point‐of‐interest (POI) group recommender systems, suggesting the most suitable visit places for a heterogeneous group in which members are far from each other would be difficult in terms of finding a consensus among group members. In this article, we argue that the geographical proximity of POIs to users' locations has a notable influence on group decisions to visit the POI and their check‐in behavior. We develop a new geographical model based on the check‐in behavior of the group in location‐based social networks to improve group recommendations by introducing a new concept called users' spatial ratio in a group vectors and using a 2D kernel density estimation method. To evaluate the performance of the approach, experimental studies were conducted on a real dataset of users and group check‐in activities collected from Foursquare Swarm. In our experiments, the proposed method makes better recommendations compared with other existing approaches. Besides, analyzing group check‐ins shows that in a group visit, the distance between the most visited place by a group member alone and the places visited by the group follows a generalized gamma distribution. Also, the ratio of this distance for the group member to the distance of another member depends on the group size.
Association between adenovirus infection and mortality outcome among pediatric patients after hematopoietic stem cell transplant
Authors: Wiriyachai Thakoon , Chaya Weerapong , Anurathapan Usanarat , Rattanasiri Sasivimol , Boonsathorn Sophida , Chaisavaneeyakorn Sujittra , Techasaensiri Chonnamet , Apiwattanakul Nopporn 
Published: October 2021

AbstractBackgroundAdenovirus can cause severe diseases in post‐hematopoietic stem cell transplant (HSCT) patients. Because these patients also have many other factors contributing to mortality, it remains controversial whether adenovirus infection itself contributes to increased mortality in these patients.ObjectiveTo determine if adenovirus infection contributes to mortality in pediatric post‐HSCT patients.MethodsThis retrospective cohort study was performed in post HSCT patients, aged 0–18 years old, admitted at Ramathibodi Hospital from 2016 to 2020. Adenovirus infection was defined as the detection of adenovirus in blood or urine by polymerase chain reaction. Multivariate cox regression was used to identify factors associated with death.ResultsThe incidence of overall adenovirus infection (viremia or viruria) in this cohort was 20.8% (26 out of 125 enrolled patients). From the multivariate cox regression analysis, overall adenovirus infection was not significantly associated with death (hazard ratio [HR]: 2.41; 95% confidence interval [CI]: 0.96–6.06;p = .060). However, presence of viremia (HR: 3.90; 95% CI: 1.40–10.86;p = .009), having maximal serum viral load > 10 000 copies/ml (HR: 3.70; 95% CI: 1.20–11.38;p = .023), presence of end‐organ diseases (HR: 3.44; 95% CI: 1.18–10.01;p = .023) were associated with mortality. Underlying diseases requiring long‐term immunosuppressive drugs before HSCT, invasive fungal disease, invasive bacterial infection, cytomegalovirus infection, and longer engraftment time were also associated with mortality.ConclusionOverall adenovirus infection does not appear to play a significant role in mortality in pediatric post‐HSCT patients. However, more invasive forms of adenovirus infection were associated with mortality in these patients.
TCP7 interacts with Nuclear Factor‐Ys to promote flowering by directly regulating SOC1 in Arabidopsis
Authors: Li Xiaoyun , Zhang Guofang , Liang Yahong , Hu Lin , Zhu Bonan , Qi Dongmei , Cui Sujuan , Zhao Hongtao 
Published: October 2021

SUMMARYThe success of plant reproduction depends on the timely transition from the vegetative phase to reproductive growth, a process often referred to as flowering. Although several plant‐specific transcription factors belonging to the Teosinte Branched 1/Cycloidea/Proliferating Cell Factor (TCP) family are reportedly involved in the regulation of flowering in Arabidopsis, the molecular mechanisms, especially for Class I TCP members, are poorly understood. Here, we genetically identified Class I TCP7 as a positive regulator of flowering time. Protein interaction analysis indicated that TCP7 interacted with several Nuclear Factor‐Ys (NF‐Ys), known as the ‘pioneer’ transcription factors; CONSTANS (CO), a main photoperiod regulator of flowering. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was differentially expressed in the dominant‐negative mutant of TCP7 (lcu) and the loss‐of‐function mutant of Class I TCP members (septuple). Additionally, we obtained genetic and molecular evidence showing that TCP7 directly activates the flowering integrator gene, SOC1. Moreover, TCP7 synergistically activated SOC1 expression upon interacting with CO and NF‐Ys in vivo. Collectively, our results provide compelling evidence that TCP7 synergistically interacts with NF‐Ys to activate the transcriptional expression of the flowering integrator gene SOC1.
Practical Method for Burner Staging Turbine Forced Response Evaluation
Authors: Kafedzhiyski Nikola , Mayorca Maria 
Published: October 2021

Abstract
Decarbonization and sustainability efforts challenge gas turbine engineers to come up with creative strategies for reduction of emissions and efficiency increase over the whole operating range. Burner staging at part loads presents a flexible solution to achieve these goals through selective burner deactivation. Shutting off burners could also be required for combustion of increased H2 content at some conditions. Burner staging will create circumferential unevenness with patterns of hot and cold streaks that could excite blade rows through the entire turbine. This paper presents a parametric method for annular combustor staging patterns' profile generation intended for use for forced response predictions from a limited number of combustor computational fluid dynamics (CFD) calculations while keeping the key phenomenological features. Two cases with burner staging turbine inlet temperature (TIT) distributions are considered and compared to a base case with uniform temperature distribution. The unsteady aerodynamic forcing was obtained from full wheel time marching unsteady CFD calculations. The results show that the hot streaks generate important and noticeable excitation sources. Additionally, the results show that the pattern generator could be used extensively before and after the unsteady calculations' phase to minimize the excitation levels and the computational load.
Nondestructive Photoelastic and Machine Learning Characterization of Surface Cracks and Prediction of Weibull Parameters for Photovoltaic Silicon Wafers
Authors: Rowe Logan P. , Kaczkowski Alexander J. , Lin Tung-Wei , Horn Gavin P. , Johnson Harley T. 
Published: October 2021

Abstract
A nondestructive photoelastic method is presented for characterizing surface microcracks in monocrystalline silicon wafers, calculating the strength of the wafers, and predicting Weibull parameters under various loading conditions. Defects are first classified through thickness infrared photoelastic images using a support vector machine-learning algorithm. Characteristic wafer strength is shown to vary with the angle of applied uniaxial tensile load, showing greater strength when loaded perpendicular to the wire speed direction than when loaded along the wire speed direction. Observed variations in characteristic strength and Weibull shape modulus with applied tensile loading direction stem from the distribution of crack orientations and the bulk stress field acting on the microcracks. Using this method, it is possible to improve manufacturing processes for silicon wafers by rapidly, accurately, and nondestructively characterizing large batches in an automated way.
Assessing the Impact of Climate Change on the Fatigue Life of Offshore Structures
Authors: Mosquera-Mosquera I. A. , Sagrilo Luis V. S. , Videiro Paulo M. , de Sousa Fernando J. M. 
Published: October 2021

Abstract
Design life of offshore structures is in general in the 20- to 30-year range, with some cases going up to 50 years. Fatigue is one of the major design criteria for such structures. Climate change may affect the fatigue life of offshore structures, it would be necessary to update the design procedures to take into account climate change effects on structural performance. This paper aims to investigate the impact of climate change in the long-term fatigue life of offshore structures due to wave loading. For this purpose, available environmental conditions for two locations (South East Brazilian Coast and North Atlantic Ocean) generated by the HadGEM-2S global climate model, considering representative concentration pathway (RCP) 4.5 and RCP 8.5 future scenarios and the historical (past) scenarios are considered. The assessment in both locations is performed for two structural models: an idealized stress spectrum for a generic fatigue hot-spot and a steel lazy wave riser (SLWR) connected to a floating production storage and offloading (FPSO). Fatigue life is estimated using the S–N curve approach. Results show that the impact on the fatigue life depends on the structure dynamic characteristics, on the geographic location and mainly on the greenhouse emission scenario. In general, for the Brazilian location, when compared to the historical scenario, most of the future scenarios lead to slightly higher fatigue damages (lower fatigue lives). On the other hand, for the North Atlantic location, there is not a clear trend for future climate change scenarios.
Determinants of Physical Activity at 90 Days After Acute Stroke or Transient Ischemic Attack in Patients With Home Discharge: A Pilot Study
Authors: Yokota Chiaki , Ohta Sachiko , Fujimoto Yasuyuki 
Published: October 2021

The aim was to identify the barriers to achieving premorbid physical activity in patients with home discharge after acute minor stroke or transient ischemic attack. Fifty-six patients (median age, 72 years) were analyzed. We assessed total physical activity in the premorbid condition and at 90 days after onset using the International Physical Activity Questionnaire. The patients were divided into two groups according to changes in total physical activity until 90 days after onset: decreased activity (n = 16) and nondecreased activity (n = 40) groups. Outcome measures were examined at discharge. The decreased activity group took significantly longer to perform the timed up and go test (median, 7.19 vs. 6.52 s) and contained more apathetic patients (44% vs. 15%). Apathy at discharge (relative risk 6.05, 95% confidence interval [1.33, 27.6]) was a significant determinant of decreased physical activity. Apathy is a barrier to the restoration of premorbid physical activity in stroke survivors.
COVID-19: responding to a pandemic on Operation TORAL
Authors: Webster Stacey , Gough A , Riley M R , Makin S 
Published: October 2021

Operation TORAL was the UK’s contribution to NATO’s Operation RESOLUTE SUPPORT in Kabul, Afghanistan. Approximately 1000 British troops were deployed in Kabul when the arrival of the COVID-19 pandemic in Afghanistan was declared. This article will describe the challenges faced due to COVID-19 in Kabul.Medical planning considerations, occupational health issues, implementation of behaviour change and operating as part of a multinational organisation are all discussed, with challenges encountered detailed and potential solutions offered. The use of a suggested framework for ensuring the medical estimate process covered all areas relevant to an emerging viral pandemic —the 4Ds and 4Cs approach—proved particularly useful in the early stages of the pandemic in Afghanistan.
Is there a role for physical activity when treating patients with cancer with immune checkpoint inhibitors? Protocol for a scoping review
Authors: Chen Miaoqi , Rai Ridesh , Fox Louis , Moss Charlotte Louise , George Gincy , Karagiannis Sophia N , Enting Deborah , Joseph Magdalene , Peat Nicola , Russell Beth , Van Hemelrijck Mieke 
Published: October 2021

IntroductionFor patients with cancer, immune checkpoint inhibitors (ICIs) produce superior long-term responses compared with alternative treatments, although at the cost of manifesting adverse immune-related events. There are many hypotheses of the impacts of physical activities in immunotherapy, but little is known about the oncological outcomes and the underlying mechanisms. This scoping review aims to identify possible physical activity interventions, their efficacy and feasibility and the potential underlying biological mechanisms responsible for their effects.Method and analysisThe Levac methodology framework was used along with guidance from the Joanna Briggs Institute Manual for Evidence Synthesis to inform development of this protocol. Abstracts and titles followed by full-text screening will be performed by two independent reviewers for inclusion. All studies describing the impact of physical activities and exercise interventions on cancer ICIs, with particular focus on oncological outcomes, quality of life or underling biological mechanisms, will be included. After extracting qualitative and quantitative data, they will be evaluated and summarised, respectively. Subsequently, a further consultation step with other scientists and healthcare professionals will be performed.Ethics and disseminationThe research findings will be published through an open-access peer-reviewed journal. The results of this scoping review will be used to inform further studies on physical impacts on immunotherapy. All data included will be from open resources, therefore, no ethical clearances are required.
Physics potential for the H$$\rightarrow \hbox {ZZ}^{*}$$ decay at the CEPC
Authors: Kiuchi Ryuta , Gu Yanxi , Zhong Min , Kong Lingteng , Schuy Alex , Hsu Shih-Chieh , Shi Xin , Zhang Kaili 
Published: October 2021

AbstractThe precision of the yield measurement of the Higgs boson decaying into a pair of Z bosons process at the Circular Electron Positron Collider is evaluated. Including the recoil Z boson associated with the Higgs production (Higgsstrahlung) a total of three Z bosons are involved for this channel, from which final states characterized by the presence of a pair of leptons, quarks, and neutrinos are chosen for the signal. Two analysis approaches are compared and the final statistical precision of $${\sigma }_{\mathrm {ZH}}{\cdot }$$

σ
ZH

·

BR($$H \rightarrow ZZ^{*}$$

H
→
Z

Z

∗

) is estimated to be 6.9% using a multivariate analysis technique, based on boosted decision trees. The relative precision of the Higgs boson width, using this $$H \rightarrow ZZ^{*}$$

H
→
Z

Z

∗

decay topology, is estimated by combining the obtained result with the precision of the inclusive ZH cross section measurement.
An Updated Experimental Evaluation of Graph Bipartization Methods
Authors: Goodrich Timothy D. , Horton Eric , Sullivan Blair D. 
Published: October 2021

We experimentally evaluate the practical state-of-the-art in graph bipartization (Odd Cycle Transversal (OCT)), motivated by the need for good algorithms for embedding problems into near-term quantum computing hardware. We assemble a preprocessing suite of fast input reduction routines from the OCT and Vertex Cover (VC) literature and compare algorithm implementations using Quadratic Unconstrained Binary Optimization problems from the quantum literature. We also generate a corpus of frustrated cluster loop graphs, which have previously been used to benchmark quantum annealing hardware. The diversity of these graphs leads to harder OCT instances than in existing benchmarks.
In addition to combinatorial branching algorithms for solving OCT directly, we study various reformulations into other NP-hard problems such as VC and Integer Linear Programming (ILP), enabling the use of solvers such as CPLEX. We find that for heuristic solutions with time constraints under a second, iterative compression routines jump-started with a heuristic solution perform best, after which point using a highly tuned solver like CPLEX is worthwhile. Results on exact solvers are split between using ILP formulations on CPLEX and solving VC formulations with a branch-and-reduce solver. We extend our results with a large corpus of synthetic graphs, establishing robustness and potential to generalize to other domain data. In total, over 8,000 graph instances are evaluated, compared to the previous canonical corpus of 100 graphs.
Finally, we provide all code and data in an open source suite, including a Python API for accessing reduction routines and branching algorithms, along with scripts for fully replicating our results.
Circulating Tumor DNA in Stage III Colorectal Cancer, beyond Minimal Residual Disease Detection, toward Assessment of Adjuvant Therapy Efficacy and Clinical Behavior of Recurrences
Authors: Henriksen Tenna Vesterman , Tarazona Noelia , Frydendahl Amanda , Reinert Thomas , Gimeno-Valiente Francisco , Carbonell-Asins Juan Antonio , Sharma Shruti , Renner Derrick , Hafez Dina , Roda Desamparados , Huerta Marisol , Roselló Susana , Madsen Anders Husted , Løve Uffe S. , Andersen Per Vadgaard , Thorlacius-Ussing Ole , Iversen Lene Hjerrild , Gotschalck Kåre Andersson , Sethi Himanshu , Aleshin Alexey , Cervantes Andres , Andersen Claus Lindbjerg 
Published: October 2021

Abstract

Purpose:
Sensitive methods for risk stratification, monitoring therapeutic efficacy, and early relapse detection may have a major impact on treatment decisions and patient management for stage III colorectal cancer patients. Beyond assessing the predictive power of postoperative ctDNA detection, we explored the added benefits of serial analysis: assessing adjuvant chemotherapy (ACT) efficacy, early relapse detection, and ctDNA growth rates.

Experimental Design:
We recruited 168 patients with stage III colorectal cancer treated with curative intent at Danish and Spanish hospitals between 2014 and 2019. To quantify ctDNA in plasma samples (n = 1,204), 16 patient-specific somatic single-nucleotide variants were profiled using multiplex-PCR, next-generation sequencing.

Results:
Detection of ctDNA was a strong recurrence predictor postoperatively [HR = 7.0; 95% confidence interval (CI), 3.7–13.5; P &lt; 0.001] and directly after ACT (HR = 50.76; 95% CI, 15.4–167; P &lt; 0.001). The recurrence rate of postoperative ctDNA-positive patients treated with ACT was 80% (16/20). Only patients who cleared ctDNA permanently during ACT did not relapse. Serial ctDNA assessment after the end of treatment was similarly predictive of recurrence (HR = 50.80; 95% CI, 14.9–172; P &lt; 0.001), and revealed two distinct rates of exponential ctDNA growth, slow (25% ctDNA-increase/month) and fast (143% ctDNA-increase/month; P &lt; 0.001). The ctDNA growth rate was prognostic of survival (HR = 2.7; 95% CI, 1.1–6.7; P = 0.039). Serial ctDNA analysis every 3 months detected recurrence with a median lead-time of 9.8 months compared with standard-of-care computed tomography.

Conclusions:
Serial postoperative ctDNA analysis has a strong prognostic value and enables tumor growth rate assessment. The novel combination of ctDNA detection and growth rate assessment provides unique opportunities for guiding decision-making.
See related commentary by Morris and George, p. 438
IgE-Based Therapeutic Combination Enhances Antitumor Response in Preclinical Models of Pancreatic Cancer
Authors: Markov Spas Dimitrov , Caffrey Thomas C. , O'Connell Kelly A. , Grunkemeyer James A. , Shin Simon , Hanson Ryan , Patil Prathamesh P. , Shukla Surendra K. , Gonzalez Daisy , Crawford Ayrianne J. , Vance Krysten E. , Huang Ying , Eberle Kirsten C. , Radhakrishnan Prakash , Grandgenett Paul M. , Singh Pankaj K. , Madiyalakan Ragupathy , Daniels-Wells Tracy R. , Penichet Manuel L. , Nicodemus Christopher F. , Poole Jill A. , Jaffee Elizabeth M. , Hollingsworth Michael A. , Mehla Kamiya 
Published: October 2021

AbstractPancreatic ductal adenocarcinoma (PDAC) represents 3% of all cancer cases and 7% of all cancer deaths in the United States. Late diagnosis and inadequate response to standard chemotherapies contribute to an unfavorable prognosis and an overall 5-year survival rate of less than 10% in PDAC. Despite recent advances in tumor immunology, tumor-induced immunosuppression attenuates the immunotherapy response in PDAC. To date, studies have focused on IgG-based therapeutic strategies in PDAC. With the recent interest in IgE-based therapies in multiple solid tumors, we explored the MUC1-targeted IgE potential against pancreatic cancer. Our study demonstrates the notable expression of FceRI (receptor for IgE antibody) in tumors from PDAC patients. Our study showed that administration of MUC1 targeted-IgE (mouse/human chimeric anti-MUC1.IgE) antibody at intermittent levels in combination with checkpoint inhibitor (anti-PD-L1) and TLR3 agonist (PolyICLC) induces a robust antitumor response that is dependent on NK and CD8 T cells in pancreatic tumor-bearing mice. Subsequently, our study showed that the antigen specificity of the IgE antibody plays a vital role in executing the antitumor response as nonspecific IgE, induced by ovalbumin (OVA), failed to restrict tumor growth in pancreatic tumor-bearing mice. Utilizing the OVA-induced allergic asthma-PDAC model, we demonstrate that allergic phenotype induced by OVA cannot restrain pancreatic tumor growth in orthotopic tumor-bearing mice. Together, our data demonstrate the novel tumor protective benefits of tumor antigen-specific IgE-based therapeutics in a preclinical model of pancreatic cancer, which can open new avenues for future clinical interventions.