bluuebunny/crossref_metadata_2025_split huggingface dataset:
Position Information in Transformers: An Overview
Authors: Dufter Philipp , Schmitt Martin , Schütze Hinrich 
Published: June 2022

Abstract
Transformers are arguably the main workhorse in recent natural language processing research. By definition, a Transformer is invariant with respect to reordering of the input. However, language is inherently sequential and word order is essential to the semantics and syntax of an utterance. In this article, we provide an overview and theoretical comparison of existing methods to incorporate position information into Transformer models. The objectives of this survey are to (1) showcase that position information in Transformer is a vibrant and extensive research area; (2) enable the reader to compare existing methods by providing a unified notation and systematization of different approaches along important model dimensions; (3) indicate what characteristics of an application should be taken into account when selecting a position encoding; and (4) provide stimuli for future research.
Sensitivity of Sparse Codes to Image Distortions
Authors: Luther Kyle , Seung H. Sebastian 
Published: June 2022

Abstract
Sparse coding has been proposed as a theory of visual cortex and as an unsupervised algorithm for learning representations. We show empirically with the MNIST data set that sparse codes can be very sensitive to image distortions, a behavior that may hinder invariant object recognition. A locally linear analysis suggests that the sensitivity is due to the existence of linear combinations of active dictionary elements with high cancellation. A nearest-neighbor classifier is shown to perform worse on sparse codes than original images. For a linear classifier with a sufficiently large number of labeled examples, sparse codes are shown to yield higher accuracy than original images, but no higher than a representation computed by a random feedforward net. Sensitivity to distortions seems to be a basic property of sparse codes, and one should be aware of this property when applying sparse codes to invariant object recognition.
Toward a Biomimetic Neural Circuit Model of Sensory-Motor Processing
Authors: Lisberger Stephen G. 
Published: June 2022

Abstract
Computational models have been a mainstay of research on smooth pursuit eye movements in monkeys. Pursuit is a sensory-motor system that is driven by the visual motion of small targets. It creates a smooth eye movement that accelerates up to target speed and tracks the moving target essentially perfectly. In this review of my laboratory's research, I trace the development of computational models of pursuit eye movements from the early control-theory models to the most recent neural circuit models. I outline a combined experimental and computational plan to move the models to the next level. Finally, I explain why research on nonhuman primates is so critical to the development of the neural circuit models I think we need.
Acceptability of reducing sedentariness using a mobile-phone application based on ‘if then’ plans for people with psychosis: A focus-group study conducted in North West England, UK
Authors: Bailey Rachel , Bartlett Y Kiera , Hassan Lamiece , Armitage Christopher J , Stockton-Powdrell Charlotte , Machin Matthew , Lewis Shon , Epton Tracy 
Published: June 2022

Objective: To understand the acceptability of (a) reducing sedentary-behaviour in people with psychosis using ‘if-then’ plans and (b) the proposed app content. Design: Qualitative acceptability study. Method: Three structured focus-groups and an interview were conducted with eight participants who had experience of a psychotic episode. They discussed sedentary-behaviour, being more active, critical situations in which they may be tempted to be sedentary and solutions to these (the if-then plans), and a mock-up of the mobile application. The Theoretical Framework of Acceptability (TFA) was used to analyse qualitatively the transcripts. Results: All TFA constructs were coded in each of the transcripts. The idea of reducing sedentary-behaviour was acceptable to people with psychosis, participants knew the importance of being more active, however it is not always their main priority. Likewise, the proposed content of the app was found to be acceptable, with participants already using some of the proposed solutions. Conclusion: This was the first study to use the TFA framework to assess the acceptability of an app that uses critical situations and solutions (‘if-then plans’) to help reduce sedentary behaviour for people with psychosis. In this sample (male, English speaking mainly white people), participants understood the benefits of being more active. However, reducing sedentary-behaviour is not the main priority of this population and being sedentary has benefits when their mental-health is bad.
Kaposi Sarcoma of the Larynx: A Systematic Review
Authors: Barron Kendyl , Omiunu Ariel , Celidonio Joseph , Cruz‐Mullane Alexandra , Din‐Lovinescu Corina , Chemas‐Velez Maria Manuela , Baredes Soly , Eloy Jean Anderson , Fang Christina H. 
Published: June 2022

AbstractObjectiveKaposi sarcoma (KS) of the larynx is a rare disease with few cases reported in the literature. This study aims to provide a comprehensive review of laryngeal KS, including patient characteristics, treatment, and clinical outcomes.Data SourcesPubMed, CINAHL, SCOPUS, and Cochrane Library.Review MethodsA systematic review of the published English literature was conducted. An electronic search and bibliographic examination of articles pertaining to laryngeal KS were performed. Demographic data, tumor site, treatment strategies, follow‐up, and outcome were analyzed.ResultsA total 77 cases from 50 articles were included in the review. The mean age was 47.6 years (range, 8‐81). There was an 8.6:1 male:female ratio. The most common presenting symptoms were dyspnea (n = 35) and hoarseness (n = 25). Laryngeal KS arose most frequently in the supraglottic region (n = 16). Chemotherapy alone (n = 27) was the most common treatment modality in patients with AIDS‐associated KS, and surgical excision alone (n = 7) was most common in patients with other subtypes of KS (eg, classic, transplant associated). Average follow‐up was 20.4 months (range, 0.75‐120). Most patients with AIDS‐associated KS died of other causes (n = 25), but most patients with other subtypes of KS were alive with no evidence of disease at follow‐up (n = 13).ConclusionThis review contains the largest pool of laryngeal KS cases to date. Long‐term outcomes were generally unfavorable, often due to advanced HIV disease at the time of diagnosis.
Pediatric Nemaline Myopathy: A Systematic Review Using Individual Patient Data
Authors: Christophers Briana , Lopez Michael A. , Gupta Vandana A. , Vogel Hannes , Baylies Mary 
Published: June 2022

Nemaline myopathy is a skeletal muscle disease that affects 1 in 50 000 live births. The objective of this study was to develop a narrative synthesis of the findings of a systematic review of the latest case descriptions of patients with NM. A systematic search of MEDLINE, Embase, CINAHL, Web of Science, and Scopus was performed using Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines using the keywords pediatric, child, NM, nemaline rod, and rod myopathy. Case studies focused on pediatric NM and published in English between January 1, 2010, and December 31, 2020, in order to represent the most recent findings. Information was collected about the age of first signs, earliest presenting neuromuscular signs and symptoms, systems affected, progression, death, pathologic description, and genetic changes. Of a total of 385 records, 55 case reports or series were reviewed, covering 101 pediatric patients from 23 countries. We review varying presentations in children ranging in severity despite being caused by the same mutation, in addition to current and future clinical considerations relevant to the care of patients with NM. This review synthesizes genetic, histopathologic, and disease presentation findings from pediatric NM case reports. These data strengthen our understanding of the wide spectrum of disease seen in NM. Future studies are needed to identify the underlying molecular mechanism of pathology, to improve diagnostics, and to develop better methods to improve the quality of life for these patients.
Understanding COVID-19 Situation in Nepal and Implications for SARS-CoV-2 Transmission and Management
Authors: Dawadi Prabin , Syangtan Gopiram , Lama Bhupendra , Kanel Sushil R. , Raj Joshi Dev , Pokhrel Lok R. , Adhikari Rameshwar , Joshi Hem R. , Pavel Ioana 
Published: June 2022

Background: The pandemic of Coronavirus Disease 2019 (COVID-19), one of the most infectious diseases in the modern history, is caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) and has had a profound health and economic toll, globally. This paper identifies the overall health status associated with COVID-19 pandemic in all 7 provinces of Nepal, a developing country in South Asia, analyzing data from January 2020 to February 2022. It focuses on the SARS-CoV-2 prevalence, transmission through wastewater and other routes, diagnostics, treatment options, and alternative medicines, thereby offering key perspectives for its management. Materials and Methods: Studies regarding coronavirus spanning the 2017 to 2022 period were searched on the web, Nepalese database, and Web of Science. Refined criteria included SARS-CoV-2 in wastewater of Nepal or worldwide. Demographic data (sex, age-group, and geographic location) were also obtained from websites and relevant reports of the Ministry of Health and Population (MOHP) of Nepal, ranging from January 2020 to February 2022. Moreover, trends concerning lockdown, business, and border activities in Nepal between February 2020 and October 2020 were evaluated. The viral dissemination pathways, diagnosis, and available treatment options, including the Ayurvedic medicine, were also examined. Results: Aerosols generated during the hospital, industrial, recreational, and household activities were found to contribute to the propagation of SARS-CoV-2 into environmental wastewater, thereby putting the surrounding communities at risk of infection. When lockdown ended and businesses opened in October 2020, the number of active cases of COVID-19 increased exponentially. Bagmati Province had the highest number of cases (53.84%), while the remaining 6 provinces tallied 46.16%. Kathmandu district had the highest number of COVID-19 cases (138, 319 cases), while Manang district had the smallest number of infections (81 cases). The male population was found to be predominantly infected (58.7%). The most affected age groups were the 31 to 40 years old males (25.92%) and the 21 to 30 years old females (26.85%). Conclusion: The pandemic impacted the public health and economic growth in our study duration. SARS-CoV-2 was prevalent in the wastewater of Nepal. The Terai districts and the megacities were mostly affected by SARS-CoV-2 infections. Working-age groups and males were identified as the highest risk groups. More investigations on the therapeutic and alternative cures are recommended. These findings may guide the researchers and professionals with handling the COVID-19 challenges in developing countries such as Nepal and better prepare for future pandemics.
Use of Computed Tomography-Guided Percutaneous Biopsy of Invasive Non-Mucinous Lung Adenocarcinoma to Predict the Degree of Histological Differentiation
Authors: Liu Dehao , Chen Lichun , Wang Xiaoping , Lin Yikai , Gu Jianwei 
Published: June 2022

Background: The International Association for the Study of Lung Cancer (IASLC) published a grading system for invasive pulmonary adenocarcinoma that is closely associated with prognosis. This study aimed to investigate the accuracy of computed tomography (CT)-guided biopsy specimen grading and surgery-guided grading systems for detecting invasive non-mucinous lung adenocarcinoma and to determine whether CT-guided biopsy can predict the degree of histological differentiation. Methods: In total, 130 patients with invasive non-mucinous lung adenocarcinoma who underwent CT-guided biopsy before surgical excision were retrospectively studied. Biopsy and surgical specimen pathologies were compared. Grading was performed according to different subtypes proposed by the International Association for the Study of Lung Cancer. Sensitivity, specificity, positive and negative predictive values (PPV/NPV), and accuracy were calculated for each subtype and grade. Results: The concordance rates of biopsy and surgical pathology subtypes and grades were 73.1% and 72.3%, respectively. Sensitivity, specificity, PPV, NPV, and accuracy of grade 3 were 54.8%, 100%, 100%, 87.6%, and 89.2%, respectively. Pathology grades were primarily discrepant with respect to two aspects of biopsy and surgical samples in the same patient. First, the biopsy and surgical specimen pathology findings indicated lepidic and acinar subtypes as the main subtypes in the same patient, respectively. Second, biopsy specimen histology did not find solid types; however, >20% of solid subtypes were identified in surgical pathology samples in the same patient. Conclusions: The preoperative CT-guided biopsy specimen grading system showed relatively high accuracy and could predict the prognosis of invasive non-mucinous lung adenocarcinoma.
Embedding patient and public involvement in dementia research: Reflections from experiences during the ‘Journeying through Dementia’ randomised controlled trial
Authors: Beresford-Dent Jules , Sprange Kirsty , Mountain Gail , Mason Clare , Wright Jessica , Craig Claire , Birt Linda 
Published: June 2022

Background The involvement of people with a diagnosis of dementia in patient and public involvement and engagement (PPIE) in research is an emerging field in the delivery of studies. Researchers need to understand and use the learning derived from various projects so that this growing body of knowledge can be applied in future research. Objective To embed PPIE throughout a randomised controlled trial of a psychosocial intervention called Journeying through Dementia. We identify and discuss the approaches to involvement that worked well and those where improvements were indicated. Design The Guidance for Reporting Involvement of Patients and the Public Short Form (GRIPP2-SF) is used to describe and critically appraise the approaches taken and the impact of PPIE involvement upon study processes, the study team and those people with dementia and their supporters who acted as advisors. Findings The involvement of people with a diagnosis of dementia and supporters as study advisors improved the accessibility and relevance of the research for people living with dementia. It also highlighted issues that researchers may have otherwise overlooked. Successful engagement of people with dementia and their supporters in the study was associated with staff skills and particularly use of techniques to scaffold meaningful involvement, as well as participants’ memory and cognitive capacity. However, embedding robust and meaningful involvement processes required significant time and resources. Discussion We propose that certain research processes need to be adapted to be accessible and appropriate for people living with dementia. Recruitment of PPIE advisors needs to reflect population diversity. There also needs to be greater parity of voice between people with lived experience of dementia and researchers. These steps will increase the impact of PPIE in research and improve the experience for those who volunteer to be PPIE advisors.
Melatonin Reduces Apoptosis Resistance of Hepatocellular Carcinoma Cells by Inhibiting BMAL1
Authors: Wang Anqi , Zhou Bei , Zhu Yue , Tan Chaisheng , Xu Jing , Cui Jie , Zhang Li , Sun Guoping 
Published: June 2022

Purpose: This study aimed to explore the role and molecular mechanism of brain and muscle ARNT-like protein 1 (BMAL1) in hepatocellular carcinoma (HCC), and the effect of melatonin on BMAL1 expression and apoptosis of HCC cells. Methods: We mainly used immunohistochemistry, western blot, cck-8 assays, flow cytometry, wound-healing assay, transwell assay, and RT-qPCR for this research. Results: The expression of BMAL1 protein was frequently up-regulated in the tissues and cell lines of HCC patients. Its high expression was significantly associated with tumor size, tumor differentiation degree, and shorter survival. In addition, cell functional experiments showed that BMAL1 could promote proliferation and migration, and inhibit apoptosis in HCC cell lines. Furthermore, the expression of BMAL1 was related to the endoplasmic reticulum stress (ERS) level. Knockdown of BMAL1 could inhibit the expression of ERS-related protein, while overexpression of BMAL1 led to the increase of ERS-related protein’s level. Low concentration of ERS led to the increase of BMAL1, and a certain degree of ERS in turn inhibited the expression of BMAL1. Melatonin promoted apoptosis of hepatoma cells by inhibiting the expression of BMAL1. Conclusion: BMAL1 plays a key role in HCC patients’ survival and tumor growth, which may be related to its interaction with ERS-related pathways. Melatonin can regulate ERS-related apoptosis resistance by inhibiting BMAL1 expression, promoting apoptosis of HCC cells.
Medicare Reimbursement in Hand and Upper Extremity Procedures: A 20-Year Analysis
Authors: Weiss Samantha N. , Gilbert Grace V. , Gentile Pietro , Gaughan John P. , Miskiel Sandra , Pagliaro Andre , Ramirez Rey , Fuller David A. 
Published: June 2022

Purpose: Concern exists that Medicare physician fees for procedures have decreased over the past 20 years. The Centers for Medicare & Medicaid Services (CMS) is set to re-evaluate these physician fees in the near future for concern that these procedures are overvalued. Our study sought to analyze trends in Medicare reimbursement rates from 2000 to 2019 for the top 20 most billed hand and upper extremity surgical procedures at our institution. Methods: The financial database of a single academic tertiary care center was queried to identify the Current Procedural Terminology codes most frequently utilized in orthopedic hand and upper extremity procedures in 2019. The Physician Fee Schedule Look-Up Tool from the CMS was queried for annual physician fee data. Monetary data were adjusted for inflation using the consumer price index of Urban Research Series (CPI-U-RS) and expressed in 2019 constant US dollars (USD). The average annual and total percent change in reimbursement were calculated via linear regression for all procedures ( P < .05). Results: Accounting for inflation, the total average physician reimbursement decreased by 20.9% from 2000 to 2019, with 12 of 20 codes decreasing by more than 20%. The greatest decrease pertained to arthrodesis of the wrist at 33.9%. Upon linear regression, all procedures were found to decrease annually, with arthrodesis of the wrist decreasing by an average of 2.3% annually over this period. Conclusions: Over the past 2 decades, physician reimbursement for hand and upper extremity procedures has significantly decreased.
The Protective Effects and Mechanism of Doxepin on Radiation–Induced Lung Injury in Rats
Authors: Wan Xinlong , Shi Xuan , Li Mengke , Chen Qing , Xue Chang , Li Guanghui , Huang Yeke , Yang Jingwen , Chen Chan , Wang Zhiyi , Ma Shumei , Liu Xiaodong 
Published: June 2022

Radiation-induced lung injuries (RILI) is one of the serious complications of radiotherapy posed by the damage of alveolar cells and inflammation over-reaction. We aimed to investigate the potential protective effects of doxepin on RILI (20 Gy total dose at 3 Gy/min of X-ray irradiation), as well as its underlying mechanism. For animal experiments, such parameters as Immunohistochemistry and hematoxylin and eosin (H&E) staining, WBC (white blood cell), CRP (C-reactive protein), Western blot, and q-PCR were detected. The results indicated that both survival status and weight increase of irradiated rats treated by doxepin (3 mg/kg/day, rat) were higher than those of treated with irradiation alone (Dosing started the day before irradiation). Further, histological examinations showed doxepin could tenuate the radiation injury, as indicated as alveolar inflammatory exudation and there was only mild interstitial inflammation infiltration. Western blotting and q-PCR showed that expression of NF-κβ in X group were higher than that in XMD group. For the first time, we reported doxepin functioned as a radioprotectant candidate, which provide a promising application of doxepin for protecting radiotherapy injuries.
Evaluation of the effect of using online database to enhance students’ learning of occupational therapy theories in occupational therapy education
Authors: Chien Chi-Wen , Mo Chloe , Lin Chung-Ying , Chan Wing Hei , Chan Cheuk Wing , Tang Wai Hin , Siu Chun Pong , Yip Hang Shuen 
Published: June 2022

Background Learning about occupational therapy theories is crucial to occupational therapy education, and an online database is developed to facilitate students’ learning of occupational therapy theories in this study. Aim This study was conducted to evaluate the effect of this database on users’ experiences. Methods A mixed-method approach, including surveys and focus groups, was used. First- and third-year students who had studied occupational therapy theory at a university participated in this study. Results One-hundred-and-twenty students completed the surveys, and 11 students participated in the focus groups. The students demonstrated a significant increase in the number of theories they named and their perceived understanding of theories after the semester. They rated the content, utility and satisfaction with the database in facilitating their understanding/learning of theories as moderate-good. Based on qualitative data, it appeared that the database provided specific information about occupational therapy theories and facilitated students’ learning and level of interest in learning about them. However, the first-year students who accessed the database showed a significantly decreased level of interest in learning about theories, but such the decrease was not found in the third-year students. Conclusion The study findings suggest that the use of an online database may enhance students' learning about occupational therapy theories in educational settings.
Exploring the barriers to pregnant women’s engagement in the childbirth process from Iranian midwives’ point of view: A qualitative study
Authors: Bayrami Roghieh , Baghaei Rahim 
Published: June 2022

Purpose: Pregnant women’s engagement in the childbirth process increases their satisfaction with childbirth, and in turn leads to a reduction in the frequency of cesarean sections and adverse pregnancy consequences. This study aimed to explore the barriers to pregnant women’s engagement in the childbirth process based on midwives' perspective. Methods: This qualitative study was conducted on 24 midwives working in Urmia hospitals in 2019. Data were collected through semi-structured in-depth individual interviews with the midwives. The participants were selected through purposeful sampling. Data analysis was performed using conventional content analysis with MAXQDA 10. Results: Analysis of the data resulted in two main categories “weakness of pregnant women’s participatory culture” (negative attitude of healthcare staff towards pregnant women’s engagement, ineffective relationships, insufficient engagement in respectful care, lack of pregnant women’s awareness of their rights and low health literacy of the pregnant women, and “managerial factors” (neglect of physiological childbirth aspects and hospital rules). Conclusion: Pregnant women’s participation in childbirth can be enhanced by promoting pregnant women’s participatory culture by making mothers aware of their rights and providing in-service training for healthcare staff to observe the rights and dignity of pregnant women. Moreover, the promotion of physiological childbirth and the correction of hospital rules can promote pregnant women’s engagement in childbirth.