bluuebunny/crossref_metadata_2025 huggingface dataset:
COMPUTERIZED QUALITATIVE TEXT ANALYSIS
Authors: Danilova Anna G. , Mitina Olga V.
Published: October 2021

Relevance. In applied psychology, researchers are increasingly faced with the task of analyzing large amounts of text, both verbal and visual. For these purposes, various methods of analysis have been developed and various computer programs have been created. Objective. The possibilities of computerized qualitative text analysis are analyzed. The spectrum of problems solved by various methods of qualitative text analysis is considered. Methods. The theoretical analysis of classical methods of qualitative text analysis is carried out. The specificity of the method of computerized discourse analysis is analyzed. The Internet searched for the most popular programs for qualitative text analysis, considered the main options and requirements for working in the program. Results. Methods of content-, discourse-, intent-analysis, conversion and narrative analysis are briefly characterized. The computerized discourse analysis (CMDA) approach is described. An approach to solving problems of various methods of qualitative analysis of text in computer analysis of qualitative data (Computer Assisted Qualitative Data Analysis; CAQDAS) is presented. The possibilities of some software packages developed within the CAQDAS approach are considered. Conclusions. The advantages of using computerized discourse analysis are shown. The topic of research of methodological problems accompanying the use of CAQDAS is outlined.
ESTABLISHING THE RELIABILITY AND VALIDITY OF THE DIAGNOSTICS MODEL OF PERFECTIONISM IN SPORT
Authors: Yakushina Anastasia A. , Leonov Sergey V. , Aslanova Margarita S.
Published: October 2021

Relevance: the problem of diagnosing perfectionism in sports activities is relevant for solving a large number of research issues related to the study of emotional states and factors of success in athletes, as well as practical tasks related to improving the efficiency and effectiveness of athletes. In this regard, seems to us the design of a method for diagnosing perfectionism in sports activities necessary and relevant.Objective: to test the method “Sport Multidimensional Perfectionism Scale”, and to check the reliability and structural validity of this method. Methods: testing was carried out on a sample (N = 323) of Russian athletes of different kinds of sports. In the process of adapting the questionnaire, a direct and reverse translation of the questionnaire was performed, the factor structure of the questionnaire was checked using exploratory factor analysis, the internal consistency of the questionnaire scales and convergent validity using correlation analysis. Results: a five-factor model of the method was identified. It include the following scales: “Organization and high personal standards“, “High parental expectations”, “Doubts about actions“, “ Concern over mistakes” and “High coaching expectations”. Analysis of the reliability of the scales showed significant internal consistency of each of them. To assess convergent validity, a correlation analysis of the scales of the tested method and the “Three-factor perfectionism questionnaire” by N. G. Garanyan and A. B. Kholmogorova was performed. The results of the analysis showed that the method “Multidimensional perfectionism scale in sports” has the high convergent validity, which indicates a fairly predictive value of this tool. Conclusions: for the first time in the field of Russian sports psychology, a tool for measuring perfectionism in athletes has been tested, which has shown high structural validity and reliability. In this regard, the method “Multidimensional perfectionism scale in sports” can be used for practical purposes to solve diagnostic and psychotherapeutic problems in the field of professional sports.
The Starting-Points for Knowledge
Authors: Shogry Simon
Published: October 2021

This paper examines some neglected Chrysippean fragments on insecure apprehension (κατάληψις). First, I present Chrysippus’ account of how non-Sages can begin to fortify their insecure apprehension and upgrade it into knowledge (ἐπιστήμη). Next, I reconstruct Chrysippus’ explanation of how sophisms and counter-arguments lead one to abandon one’s insecure apprehension. One such counter-argument originates in the sceptical Academy and targets the Stoic claim that insecure apprehension can be acquired on the basis of custom (συνήθεια). I show how Chrysippus could defend the possibility of custom-based apprehension, while also denying that there is custom-based knowledge.
In disentangling two species limits of Hechtia (Bromeliaceae: Hechtioideae) from Sierra Madre Occidental, a new species is discovered from Durango, Mexico
Authors: RAMÍREZ-MORILLO IVÓN , CARRILLO-REYES PABLO , TAPIA-MUÑOZ JOSÉ LUIS , RAMÍREZ-DÍAZ CLAUDIA J.
Published: October 2021

Epitypes are proposed for two species of Hechtia: H. subalata and H. jaliscana, both endemic to Western Mexico. The holotypes of both species consist of fruiting specimens. While the female flowers of both species are extremely similar, the staminate ones are noticeable different: we select staminate vouchers as epitypes to clearly circumscribe both taxa. As a result of the delimitation of the concept Hechtia subalata and its geographical distribution, we identify a new species from Durango, Mexico, previously misidentified as Hechtia subalata: Hechtia marthae. We provide images portraying plant parts of all species, as well as photographs in habitat. Finally, assessments of the conservation status of the three species sensu IUCN criteria are included.
Two new species of Cryptanthus (Bromelioideae, Bromeliaceae) from northeastern Brazil
Authors: FERREIRA DÉBORA MARIA CAVALCANTI , ALMEIDA ERTON MENDONÇA DE , LOUZADA RAFAEL BATISTA
Published: October 2021

Two new species of Cryptanthus from Bahia State, in northeastern Brazil, are described and illustrated. Cryptanthus apiculatantherus occurs in Atlantic Forest and Cryptanthus brevibracteatus was discovered in a transition area between Atlantic Forest and Caatinga. Cryptanthus apiculatantherus and C. bibarrensis have similar stem lengths and leaf blade shapes, but differ mainly by the stem diameter, width of the leaf sheaths, sepal and petal color, anther apex shape, and length and width of the ovary. Cryptanthus brevibracteatus and C. warren-loosei have a similar leaf blade color and are geographically close to each other, but differ by the number of flowers in the apical cluster of flowers of the inflorescence, length and width of the floral bracts, length of the sepals, connation of the sepals and length of the sepal lobes. Data about the geographic distribution, habitat, phenology, conservation status, taxonomic comments, a distribution map and photographs of the new species are provided. In addition, there are tables included that compare the new species to morphologically similar species.
Properties of coherent structures over Paris: a study based on an automated classification method for Doppler lidar observations
Authors: Cheliotis Ioannis , Dieudonné Elsa , Delbarre Hervé , Sokolov Anton , Dmitriev Egor , Augustin Patrick , Fourmentin Marc , Ravetta François , Pelon Jacques
Published: October 2021

The studies related to the coherent structures in the atmosphere, using Doppler wind lidar observations, so far relied on the manual detection and classification of the structures in the lidar images, making this process time-consuming. We developed an automated classification based on texture analysis parameters and the quadratic discriminant analysis algorithm for the detection of medium-to-large fluctuations and coherent structures recorded by single Doppler wind lidar quasi-horizontal scans. The algorithm classified a training dataset of 150 cases into four types of patterns, namely streaks (narrow stripes), rolls (wide stripes), thermals (enclosed areas) and “others” (impossible to classify), with 91% accuracy. Subsequently, we applied the trained algorithm to a dataset of 4577 lidar scans recorded in Paris, atop a 75 m tower for a 2-month period (September-October 2014). The current study assesses the quality of the classification by examining the physical properties of the classified cases. The results show a realistic classification of the data: with rolls and thermals cases mostly classified concurrently with a well-developed atmospheric boundary layer and the streaks cases associated with nocturnal low-level jets (nllj) events. Furthermore, rolls and streaks cases were mostly observed under moderate or high wind conditions. The detailed analysis of a four-day period reveals the transition between the types. The analysis of the space spectra in the direction transverse to the mean wind, during these four days, revealed streaks spacing of 200 to 400 m, and rolls sizes, as observed in the lower level of the mixed layer, of approximately 1 km.
Effect of position of radial air injection plane on control of thermo-acoustic instability using active closed-loop method
Authors: Deshmukh Nilaj N , Ansari Afzal , Kumar Praseed , George Allen V , Thomas Febin J , George Merick Steve
Published: October 2021

Thermo-acoustic instability occurs when self-excited oscillations are generated due to the coupling between unsteady heat release and acoustics. This phenomenon can result in an increased rate of vibration, structural damage, and produces unwanted emissions. Thermo-acoustic instability occurs in rocket engines, gas turbines, combustors, and furnaces. When thermo-acoustic instability occurs, many modes are developed naturally at a specific point. Some waves are unstable and some are stable. So, to study this phenomenon the most unstable waves are considered and a technique is developed to suppress these unstable waves. A radial air injector as a closed-loop active control method is used for breaking the coupling between the heat waves and acoustics inside the 1D combustion chamber. The distance between the burner and the air injector is varied for the fixed position of the burner with respect to the Rijke tube, that is, x/L = 0.01125, 0.0075, and 0.00375. This closed-loop method works based on the feedback acquired from a microphone. The control method is built using DAQ and Arduino with the LabVIEW as interface for Arduino (LIFA). An air flow rate controller setup is developed to control and measure air required for suppressing the thermo-acoustic instability. Thermo-acoustic instability is effectively suppressed with the help of radial injection in the form of micro-jets at the downstream of the burner as the closed-loop controlling method. It is concluded that when the radial micro-jet air injection plane is closer to the burner head, the thermo-acoustic instability gets suppressed in a short time and with a lesser quantity of air.
Are customer reviews just reviews? Hotel forecasting using sentiment analysis
Authors: Wu Doris Chenguang , Zhong Shiteng , Qiu Richard T R , Wu Ji
Published: October 2021

Despite the important role of the sentiment of customer reviews in the tourist decision-making process, it has received limited attention from the field of tourism demand forecasting. This study aims to examine the sentiment information of customer reviews and explore its potential in enhancing hotel demand forecast. Empirically, four Macau luxury hotels are selected and their customer reviews are crawled from two popular online platforms. A deep learning method, the Long Short-Term Memory model, is used to extract sentiment information from consumer reviews. Three sentiment indices, namely, bullish index, average index and variance index, are constructed and examined. The effectiveness of these sentiment indices is further evaluated by the autoregressive integrated moving average with exogenous variables model. Empirical results indicate that the inclusion of the sentiment indices helps with improving forecast accuracy. The findings of this study further emphasise the importance of textual content to hotel practitioners in terms of strategy formulation, revenue management and competitiveness enhancement.
The value of systematic follow-up imaging for assessing pseudoaneurysm formation after blunt and penetrating liver injury: A level 1 trauma centre experience
Authors: Patel Neeral R , Mehdi Aia S , Sandhu Amandeep , Mallon Dermot , Dick Elizabeth , Batrick Nicola , Kashef Elika
Published: October 2021

Introduction

Hepatic pseudoaneurysm (HPA) is a rare but potentially life-threatening sequelae of blunt or penetrating liver trauma. At our institution, an imaging protocol for liver injury patients has been developed, with repeat computed tomographic (CT) angiography of the liver 48–72 h post-admission to assess for HPA. The purpose of this study was to evaluate the utility of this imaging pathway in liver trauma for the detection of HPAs.

Methods

A retrospective analysis was performed on patients who were admitted to our institution between January 2014 and January 2018, found to have either blunt or penetrating liver injury on initial CT imaging. Data collection included mechanism of injury, injury severity score (ISS), American Association for the Surgery of Trauma (AAST) liver injury score, initial and follow-up CT findings and secondary intervention.

Results

During the study period, 149 major trauma patients were admitted with liver injuries (mean age 35.6 years; 72% male, 28% female). Seventy two percent of patients suffered blunt (median ISS = 29; median AAST = 2.89) and 28% patients suffered penetrating injuries (median ISS = 16; median AAST = 2.88). The mean time to follow-up CT was 46.1 h. Follow-up CT identified 8 (5.4%) HPAs. 5 (62.5%) of these patients were treated with embolization. ISS and AAST were not associated with pseudoaneurysm formation according to logistic regression analysis; however, ISS (OR 1.06 [1.02, 1.09; p < 0.05]) and AAST (OR 2.24, [1.31, 3.83; p < 0.05]) were associated with requirement for embolization.

Conclusion

Our experience indicates a role for early detection of HPAs using a dedicated trauma imaging pathway.
Association Between Blood and Lymphocyte Levels of Cyclosporin A and Infectious Complications in Renal Transplant Patients
Authors: Milane Aline , Abou-Abbas Linda , Osmani Lara , Saber Naja , Mefleh Nadine , Barbari Antoine
Published: October 2021

Objectives

This study aims to investigate a potential association between whole blood and lymphocyte Cyclosporin A (CyA) levels and the occurrence and frequency of infectious complications in kidney transplant patients.

Methods

The study involves 130 kidney transplant recipients who received CyA in addition to Mycophenolate Mofetil and steroids. CyA whole blood trough and maximum level (CyA BL0 and CyA BLm) as well as the corresponding levels in the lymphocytes (CyA L0 and CyA Lm) were measured for 6 months post-transplantation.

Results

Cytomegalovirus (CMV) as well as urinary tract infections (UTIs) were the most commonly diagnosed with an incidence of 24.6% and 26.2%, respectively. Only CyA L0 showed a significant association with CMV infection occurrence (adjusted OR = 1.051, 95% CI .997–1.025, P-value 0.046). A positive linear correlation was found between CyA BL0, CyA BLm and CyA Lm and the number of CMV episodes per patient.

Conclusion

We showed an association between the CMV infections occurrence and the trough lymphocyte level of CyA (CyA L0). Both lymphocyte CyA levels also correlated with the frequency of CMV infections. Further studies are needed to establish the optimal range of both CyA blood and lymphocyte levels and decrease the risk of opportunistic infections in high risk patients.
Legitimacy, Signature and Sovereignty in Derrida
Authors: Kitus Andro
Published: October 2021

Legitimacy is a concept that has been largely forgotten by the deconstructive discourse on law and politics. This article seeks, on the one hand, to reassess the role of legitimacy in deconstruction and, on the other hand, to bring deconstructive thinking to bear on the concept of legitimacy. By re-reading Derrida’s “Declarations of Independence” through the lenses of his later texts on sovereignty and (counter)signature, it is argued that, rather than being deconstructible, legitimacy is deconstructing any self-founding of law and power. As such, legitimacy functions not as an evaluative concept of law and order but as a constantly insisting demand that facilitates the principles of responsibility and responsiveness.
Observed Characteristics Associated with Diabetes Device Use Among Teens with Type 1 Diabetes
Authors: Chen Charlotte W. , Tinsley Liane J. , Volkening Lisa K. , Anderson Barbara J. , Laffel Lori M.
Published: October 2021

Background:

Despite advancements in diabetes technologies, disparities remain with respect to diabetes device use in youth with type 1 diabetes (T1D). We compared sociodemographic, diabetes, and psychosocial characteristics associated with device (pump and continuous glucose monitor [CGM]) use in 13- to 17-year-old teens with T1D.

Materials/Methods:

Data were derived from a multicenter clinical trial to optimize self-care and glycemic control in teens with T1D. We categorized teens as pump users versus non-users and CGM users versus non-users based on their diabetes device usage. Chi-square and t-tests compared characteristics according to device use.

Results:

The sample comprised 301 teens (50% female) with baseline mean ± SD age 15.0 ± 1.3 years, T1D duration 6.5 ± 3.7 years, and HbA1c 8.5 ± 1.1% (69 ± 12 mmol/mol). Two-thirds (65%) were pump users, and 27% were CGM users. Pump users and CGM users (vs. non-users) were more likely to have a family annual household income ≥$150,000, private health insurance, and a parent with a college education (all P < .001). Pump users and CGM users (vs. non-users) also performed more frequent daily blood glucose (BG) checks (both P < .001) and reported more diabetes self-care behaviors (both P < .05). Pump users were less likely to have baseline HbA1c ≥9% (75 mmol/mol) ( P = .005) and to report fewer depressive symptoms ( P = .02) than pump non-users. Parents of both CGM and pump users reported a higher quality of life in their youth ( P < .05).

Conclusion:

There were many sociodemographic, diabetes-specific, and psychosocial factors associated with device use. Modifiable factors can serve as the target for clinical interventions; youth with non-modifiable factors can receive extra support to overcome potential barriers to device use.
Valgus Control Feedback and Taping Improves the Effects of Plyometric Exercises in Women With Dynamic Knee Valgus
Authors: Shams Fereshteh , Hadadnezhad Malihe , Letafatkar Amir , Hogg Jennifer
Published: October 2021

Background:

Female athletes are more predisposed to anterior cruciate ligament (ACL) injuries in comparison with their male counterparts. Research on ACL injury prevention strategies has demonstrated beneficial effects of plyometric exercises and feedback (FB) during the exercises. FB has resulted in reductions in vertical ground-reaction force and kinematic risk factors associated with ACL injury. Furthermore, taping (TP) may draw attention to the restriction created by the tape and serve as real-time biofeedback. The additional influence of FB and TP on plyometric exercises has not been determined.

Hypothesis:

FB and TP interventions delivered during plyometric exercises would result in positive changes in biomechanics and muscle onset in female athletes displaying dynamic knee valgus.

Design:

Controlled trial.

Setting:

University research laboratory.

Level of Evidence:

Level 2.

Methods:

Forty-eight active female athletes were divided into 3 groups: control (n = 16), plyometric training with FB (n = 16), and plyometric training with TP (n = 16). The 2 experimental groups performed a 6-week exercise program with either FB or TP. The control group continued its regular team schedule. Knee joint position sense, landing error scoring system (LESS), and the onset of muscle activation (the point at which muscle activation exceeds 3 standard deviations over baseline and continued above this threshold for at least 25 ms) before landing for the rectus femoris, vastus medialis, vastus lateralis, gluteus medius, semitendinosus, and biceps femoris during pre- and posttests were measured.

Results:

The vastus lateralis onset later in the TP group compared with the FB group ( d [95% CI] = 0.64 [0.35-0.82], P = 0.01). Joint position sense accuracy improved only in the TP group ( d = −0.63, P = 0.001). Both the FB ( d = −0.85, P = 0.001), and TP ( d = −0.82, P = 0.001) groups improved in LESS scores.

Conclusion:

The results of the present study showed that plyometric exercises with FB or TP affect LESS and the onset of the vastus lateralis in active uninjured women with dynamic knee valgus, while TP improves joint position sense. Therefore, when more accurate joint position sense is desired, practitioners may use plyometric with TP. If an improved LESS score is desired, plyometrics with either TP or FB are acceptable.

Clinical Relevance:

Our findings indicate that female athletes may benefit more when completing a plyometric training program with a TP versus an FB. Trainers, coaches, and clinicians should consider utilizing instructions that promote an external focus when implementing plyometric training programs with male athletes.
Rapamycin-induced M2 macrophage autophagy promotes the migration and invasion of bladder cancer cells via increased IL-10 secretion
Authors: Guo Yuanyuan , Li Zhong , Cao Zhenxue , Ma Tantu , Mei Juan , Sun Wei , Gao Wuyue , Liu Beibei , Liu Jianmin , Wang Rui
Published: October 2021

Intrduction:

Rapamycin is an mTOR inhibitor and a prominent inducer of autophagy in cancer cells and tumor interstitial cells. Macrophages are the primary type of immune cells observed in the tumor microenvironment and serve varying roles in the progression of cancer by polarizing into distinct phenotypes. However, whether rapamycin-induced macrophage autophagy influences bladder cancer remains unclear.

Methods:

THP-1 cells were successfully polarized into M1 or M2 macrophages, which were identified by detecting CD86 (M1) or CD206 (M2) expressions using flow cytometry and measuring M1/M2-related mRNA expressions using reverse transcription-quantitative PCR. Rapamycin was employed for inducing autophagy, and then the influences of enhanced autophagic M1 and M2 macrophages on migration and invasion of bladder cancer cells were confirmed by wound healing and Transwell assay in the co-culture model. Furthermore, the gene and protein expressions of IL-10 and the underlying role are still unclear.

Results:

Rapamycin significantly increased autophagy levels in M1 and M2 macrophages, while only autophagy-enhanced M2 macrophages facilitated the migration and invasion of bladder cancer cells. Furthermore, rapamycin increased IL-10 secretion from M2 macrophages, which mediated the effects of M2 macrophages on migration and invasion of bladder cancer.

Conclusion:

Rapamycin induces M2 macrophage autophagy and promotes the migration and invasion of bladder cancer by increasing IL-10 secretion, suggesting that M2 macrophage autophagy is an underlying target of rapamycin in treating bladder cancer.
A Study of Teacher Performance in English for Academic Purposes Course: Evaluating Efficiency
Authors: Ghaffarian Asl Solmaz , Osam Necdet
Published: October 2021

Identifying significant factors in teaching-learning performance affecting the efficiency of teachers at university is an indispensable factor in upholding the quality of the teaching in English for Academic Purposes (EAP) courses. This study aims to evaluate teachers’ performance in EAP courses using the students’ course-instructor evaluation survey, and the students’ final grades. For this purpose, the Performance Improvement Management (PIM) software Data Envelopment Analysis (PIM-DEA) is applied to evaluate the efficiency of EAP teachers. Later, a sensitivity analysis is applied to prioritize the significant indicators of teacher performance following an interview with the teachers aimed at the betterment of their performance. The result of the study reveals that the degree of student satisfaction in relation to assignments, exams, and grading systems are significant factors related to teachers’ performance. A wider realization of this should be seen, in the researcher’s opinion, vital to the development of the educational sector.
Assessment of Anterolateral Ligament of the Knee After Primary Versus Revision Anterior Cruciate Ligament Reconstruction
Authors: Suh Dongwhan , Chang Moon Jong , Park Hyung Jun , Chang Chong Bum , Kang Seung-Baik
Published: October 2021

Background:

The anterolateral ligament of the knee (ALL) is a component of the lateral complex that stabilizes the structure against rotational force and may be associated with the outcome of anterior cruciate ligament (ACL) reconstruction (ACLR).

Purpose:

To (1) find whether the visibility of the structure of the ALL is different in primary and revision ACLR groups, (2) determine whether the abnormal findings of the ALL structure on magnetic resonance imaging (MRI) scans are associated with type of trauma in ACL injury and mode of graft failure, and (3) determine whether there are differences in knee functional scores between patients with or without abnormal findings of the ALL structure on MRI scans in primary and revision ACLR groups.

Study Design:

Cohort study; Level of evidence, 3.

Methods:

This retrospective study included 40 patients who underwent primary ACLR and 39 patients who underwent revision ACLR. Conventional MRI (1.5-T) scans taken before primary or revision ACLR were obtained and analyzed for visibility of the ALL, frequency and degree of injury of the ALL, and ALL signal anomalies. We also evaluated 1-year postoperative functional knee scores using the subjective International Knee Documentation Committee and Lysholm scores.

Results:

Visibility of the ALL was better in the primary ACLR group than the revision ACLR group (38% vs 14%; P = .041). The primary ACLR group showed a lower degree of injury across the femoral, meniscal, and tibial attachment sites than did the revision ACLR group (30% vs 13%, 41% vs 8%, and 62% vs 26%, respectively). Relative signal anomaly of the ALL was more frequent in the case of contact versus noncontact trauma of the ACL (85% vs 15%; P = .035), while absolute signal anomaly was equally observed between cases of contact and noncontact trauma in the primary ACLR group (50% vs 50%). No association was observed between ALL signal anomalies and 1-year postoperative functional knee scores.

Conclusion:

The revision ACLR group offered less visibility and showed a tendency for more frequent, higher degree of injury to the structure of the ALL. Regardless of observational differences between the 2 groups, no definite relevance was observed between the image and the functional outcome. For the assessment of the ALL, routinely performed conventional MRI alone is insufficient to make a clinical decision.
Health Starting Points: Continuity and Change in Physical and Mental Health before and during the Pandemic
Authors: Manning Wendy , Longmore Monica , Giordano Peggy , Douthat Cameron
Published: October 2021

The pandemic has created multiple changes in the lives of Americans, with growing and widespread concerns about the implications for the nation’s health and well-being. Most empirical examinations of the physical and mental health implications of the pandemic have rested on aggregate comparisons of prepandemic and pandemic indicators of health. The authors contribute to this body of work by considering continuity and change in health and well-being over time. The authors draw on respondents in a population-based sample with repeated health measures of physical health, depressive symptoms, and anxiety collected prior to the pandemic and subsequently during the pandemic. Using Sankey figures, the authors illustrate their health pathways and as a result highlight the importance of a longitudinal lens on assessments of health. The authors find health starting points are critical to understanding distribution and levels of physical and emotional health issues during the pandemic.
Deleterious protein-coding variants in diverse cattle breeds of the world
Authors: Subramanian Sankar
Published: October 2021

The domestication of wild animals has resulted in a reduction in effective population sizes, which can affect the deleterious mutation load of domesticated breeds. In addition, artificial selection contributes to the accumulation of deleterious mutations because of an increased rate of inbreeding among domesticated animals. Since founder population sizes and artificial selection differ between cattle breeds, their deleterious mutation load can vary. We investigated this question by using whole-genome data from 432 animals belonging to 54 worldwide cattle breeds. Our analysis revealed a negative correlation between genomic heterozygosity and nonsynonymous-to-silent diversity ratio, which suggests a higher proportion of single nucleotide variants (SNVs) affecting proteins in low-diversity breeds. Our results also showed that low-diversity breeds had a larger number of high-frequency (derived allele frequency (DAF) > 0.51) deleterious SNVs than high-diversity breeds. An opposite trend was observed for the low-frequency (DAF ≤ 0.51) deleterious SNVs. Overall, the number of high-frequency deleterious SNVs was larger in the genomes of taurine cattle breeds than of indicine breeds, whereas the number of low-frequency deleterious SNVs was larger in the genomes of indicine cattle than in those of taurine cattle. Furthermore, we observed significant variation in the counts of deleterious SNVs within taurine breeds. The variations in deleterious mutation load between taurine and indicine breeds could be attributed to the population sizes of the wild progenitors before domestication, whereas the variations observed within taurine breeds could be due to differences in inbreeding level, strength of artificial selection, and/or founding population size. Our findings imply that the incidence of genetic diseases can vary between cattle breeds.
Tailored graphical lasso for data integration in gene network reconstruction
Authors: Lingjærde Camilla , Lien Tonje G. , Borgan Ørnulf , Bergholtz Helga , Glad Ingrid K.
Published: October 2021

Background

Identifying gene interactions is a topic of great importance in genomics, and approaches based on network models provide a powerful tool for studying these. Assuming a Gaussian graphical model, a gene association network may be estimated from multiomic data based on the non-zero entries of the inverse covariance matrix. Inferring such biological networks is challenging because of the high dimensionality of the problem, making traditional estimators unsuitable. The graphical lasso is constructed for the estimation of sparse inverse covariance matrices in such situations, using $$L_1$$

L
1

-penalization on the matrix entries. The weighted graphical lasso is an extension in which prior biological information from other sources is integrated into the model. There are however issues with this approach, as it naïvely forces the prior information into the network estimation, even if it is misleading or does not agree with the data at hand. Further, if an associated network based on other data is used as the prior, the method often fails to utilize the information effectively.

Results

We propose a novel graphical lasso approach, the tailored graphical lasso, that aims to handle prior information of unknown accuracy more effectively. We provide an R package implementing the method, . Applying the method to both simulated and real multiomic data sets, we find that it outperforms the unweighted and weighted graphical lasso in terms of all performance measures we consider. In fact, the graphical lasso and weighted graphical lasso can be considered special cases of the tailored graphical lasso, and a parameter determined by the data measures the usefulness of the prior information. We also find that among a larger set of methods, the tailored graphical is the most suitable for network inference from high-dimensional data with prior information of unknown accuracy. With our method, mRNA data are demonstrated to provide highly useful prior information for protein–protein interaction networks.

Conclusions

The method we introduce utilizes useful prior information more effectively without involving any risk of loss of accuracy should the prior information be misleading.
Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits
Authors: Liu Dengying , Chen Zhenliang , Zhao Wei , Guo Longyu , Sun Hao , Zhu Kai , Liu Guanglei , Shen Xiuping , Zhao Xiaoduo , Wang Qishan , Ma Peipei , Pan Yuchun
Published: October 2021

Background

Over several decades, a wide range of natural and artificial selection events in response to subtropical environments, intensive pasture and intensive feedlot systems have greatly changed the customary behaviour, appearance, and important economic traits of Shanghai Holstein cattle. In particular, the longevity of the Shanghai Holstein cattle population is generally short, approximately the 2nd to 3rd lactation. In this study, two complementary approaches, integrated haplotype score (iHS) and runs of homozygosity (ROH), were applied for the detection of selection signatures within the genome using genotyping by genome-reduced sequence data from 1092 cows.

Results

In total, 101 significant iHS genomic regions containing selection signatures encompassing a total of 256 candidate genes were detected. There were 27 significant |iHS| genomic regions with a mean |iHS| score > 2. The average number of ROH per individual was 42.15 ± 25.47, with an average size of 2.95 Mb. The length of 78 % of the detected ROH was within the range of 1–2 MB and 2–4 MB, and 99 % were shorter than 8 Mb. A total of 168 genes were detected in 18 ROH islands (top 1 %) across 16 autosomes, in which each SNP showed a percentage of occurrence > 30 %. There were 160 and 167 genes associated with the 52 candidate regions within health-related QTL intervals and 59 candidate regions within reproduction-related QTL intervals, respectively. Annotation of the regions harbouring clustered |iHS| signals and candidate regions for ROH revealed a panel of interesting candidate genes associated with adaptation and economic traits, such as IL22RA1, CALHM3, ITGA9, NDUFB3, RGS3, SOD2, SNRPA1, ST3GAL4, ALAD, EXOSC10, and MASP2. In a further step, a total of 1472 SNPs in 256 genes were matched with 352 cis-eQTLs in 21 tissues and 27 trans-eQTLs in 6 tissues. For SNPs located in candidate regions for ROH, a total of 108 cis-eQTLs in 13 tissues and 4 trans-eQTLs were found for 1092 SNPs. Eighty-one eGenes were significantly expressed in at least one tissue relevant to a trait (P value < 0.05) and matched the 256 genes detected by iHS. For the 168 significant genes detected by ROH, 47 gene-tissue pairs were significantly associated with at least one of the 37 traits.

Conclusions

We provide a comprehensive overview of selection signatures in Shanghai Holstein cattle genomes by combining iHS and ROH. Our study provides a list of genes associated with immunity, reproduction and adaptation. For functional annotation, the cGTEx resource was used to interpret SNP-trait associations. The results may facilitate the identification of genes relevant to important economic traits and can help us better understand the biological processes and mechanisms affected by strong ongoing natural or artificial selection in livestock populations.
Soluble programmed death molecule 1 (sPD-1) as a predictor of interstitial lung disease in rheumatoid arthritis
Authors: Xu Li , Jiang Lichun , Nie Liuyan , Zhang Songzhao , Liu Lei , Du Yan , Xue Jing
Published: October 2021

Background

Previous studies have indicated that the programmed death molecule 1 (PD-1) signaling pathway may play a key role in rheumatoid arthritis (RA). However, the pathogenesis of rheumatoid arthritis-related interstitial lung disease (RA-ILD) is not clear. We examined the serum levels of soluble PD-1 in patients with RA and its relationship with RA-ILD.

Methods

Blood samples were obtained from 87 patients with RA (58 with ILD and 29 without ILD) and 45 healthy controls. Serum sPD-1 was measured by Enzyme-Linked Immunosorbent Assay. The pulmonary interstitial disease score was completed by a pulmonary physician and a radiologist through chest high-resolution computed tomography. Patients with RA-ILD were tested for lung function [e.g., forced vital capacity (FVC%), diffusing capacity of lungs for carbon monoxide (DLCO%)]. Associations between ILD and various markers, including sPD-1 and confounding factors, were investigated by logistic regression analysis. Diagnostic values of sPD-1 for the presence of ILD were investigated using receiver operating characteristic curve analysis.

Results

Serum sPD-1 levels were higher in RA patients with ILD than in RA patients without ILD and healthy controls (185.1 ± 109.0 pg/ml vs. 119.1 ± 77.5 pg/ml vs. 52.1 ± 21.7 pg/ml, P < 0.05). Serum sPD-1 levels were positively correlated with RF titer (P = 0.02, r = 0.249), anti-cyclic citrullinated peptide antibody status (P = 0.02, r = 0.243), and serum IgG levels (P < 0.001, r = 0.368), negatively associated with FVC% (P = 0.02, r = − 0.344), forced expiratory volume (FEV1%) (P  = 0.01, r = − 0.354), total lung capacity (TLC%) (P = 0.046, r = − 0.302), and was independently associated with the presence of ILD in RA patients by multivariate logistic regression analysis. The sensitivity and specificity of sPD-1 levels for the detection of ILD in RA patients were 58.6% and 75.9%, respectively. The area under the curve was 0.689.

Conclusion

Serum sPD-1 levels were increased in RA patients with ILD. Increased sPD-1 may be a valuable biomarker to predict the presence of ILD in patients with RA.
Longitudinal study: understanding the lived experience of couples across the trajectory of dementia
Authors: Mittelman Mary S. , O’Connor Maureen K. , Donley Tiffany , Epstein-Smith Cynthia , Nguyen Andrew , Nicholson Roscoe , Salant Rebecca , Shirk Steven D. , Stevenson Elizabeth
Published: October 2021

Background

The longitudinal study, “Couples Lived Experiences,” focuses on whether and how relationship characteristics of older couples change with the cognitive decline of one member of the couple, and how these changes affect each individual’s emotional and physical health outcomes. Until now, most psychosocial research in dementia has focused either on the person with dementia (PWD) or the caregiver separately. The previous literature examining relationship characteristics and their role in outcomes for the caregiver and PWD is scant and suffers from methodological issues that limit the understanding of which relationship characteristics most influence outcomes for caregivers and care-receivers and what other factors may mitigate or exacerbate their effects.

Methods

We will enroll 300 dyads and collect information via online interviews of each member of the couple, every 6 months for 3 years. Relationship characteristics will be measured with a set of short, well-validated, and reliable self-report measures, plus the newly developed “Partnership Approach Questionnaire.” Outcomes include global quality of life, subjective physical health, mental health (depression and anxiety), and status change (transitions in levels of care; i.e., placement in a nursing home). Longitudinal data will be used to investigate how relationship characteristics are affected by cognitive, functional, and behavioral changes, and the impact of these changes on health outcomes. Qualitative data will also be collected to enrich the interpretation of results of quantitative analyses.

Discussion

Psychosocial interventions have demonstrated effectiveness in promoting the wellbeing of PWD and their caregivers. The knowledge gained from this study can lead to the development or enhancement of targeted interventions for older couples that consider the impact of cognitive and functional decline on the relationship between members of a couple and thereby improve their wellbeing.

Trial registration

This study has been registered with ClinicalTrials.gov. ClinicalTrials.gov Identifier is:NCT04863495.
Temporal changes in cardiovascular disease and infections in dialysis across a 22-year period: a nationwide study
Authors: Kaur Kamal Preet , Chaudry Mavish Safdar , Fosbøl Emil Loldrup , Østergaard Lauge , Torp-Pedersen Christian , Bruun Niels Eske
Published: October 2021

Background

Cardiovascular diseases (CVD) and infections are recognized as serious complications in patients with end stage kidney disease. However, little is known about the change over time in incidence of these complications. This study aimed to investigate temporal changes in CVD and infective diseases across more than two decades in chronic dialysis patients.

Methods

All patients that initiated peritoneal dialysis (PD) or hemodialysis (HD) between 1996 and 2017 were identified and followed until outcome (CVD, pneumonia, infective endocarditis (IE) or sepsis), recovery of kidney function, end of dialysis treatment, death or end of study (December 31st, 2017). The calendar time was divided into 5 periods with period 1 (1996–2000) being the reference period. Adjusted rate ratios were assessed using Poisson regression.

Results

In 4285 patients with PD (63.7% males) the median age increased across the calendar periods from 65 [57–73] in 1996–2000 to 69 [55–76] in 2014–2017, (p <  0.0001). In 9952 patients with HD (69.2% males), the overall median age was 71 [61–78] without any changes over time.

Among PD, an overall non-significant decreasing trend in rate ratios (RR) of CVD was found, (p = 0,071). RR of pneumonia increased significantly throughout the calendar with an almost two-fold increase of the RR in 2014–2017 (RR 1.71; 95% CI 1.46–2.0), (p <  0.001), as compared to the reference period. The RR of IE decreased significantly until 2009 (RR 0.43; 95% CI 0.21–0.87), followed by a return to the reference level in 2010–2013 (RR 0.87; 95% CI 0.47–1.60 and 2014–2017 (RR 1.1; 95% CI 0.59–2.04). A highly significant (p <  0.001) increase in sepsis was revealed across the calendar periods with an almost 5-fold increase in 2014–2017 (RR 4.69 95% CI 3.69–5.96).

In HD, the RR of CVD decreased significantly (p <  0.001) from 2006 to 2017 (RR 0.85; 95% CI 0.79–0.92). Compared to the reference period, the RR for pneumonia was high during all calendar periods (p <  0.05). The RR of IE was initially unchanged (p = 0.4) but increased in 2010–2013 (RR 2.02; 95% CI 1.43–2.85) and 2014–2017 (RR 3.39; 95% CI 2.42–4.75). No significant changes in sepsis were seen.

Conclusion

Across the two last decades the RR of CVD has shown a decreasing trend in HD and PD patients, while RR of pneumonia increased significantly, both in PD and in HD. Temporal trends of IE in HD, and particularly of sepsis in PD were upwards across the last decades.
Test-retest reliability of physical activity questionnaires in Parkinson’s disease
Authors: Ånfors Samuel , Kammerlind Ann-Sofi , Nilsson Maria H.
Published: October 2021

Background

People with Parkinson’s disease are less physically active than controls. It is important to promote physical activity, which can be assessed using different methods. Subjective measures include physical activity questionnaires, which are easy and cheap to administer in clinical practice. Knowledge of the psychometric properties of physical activity questionnaires for people with Parkinson’s disease is limited. The aim of this study was to evaluate the test-retest reliability of physical activity questionnaires in individuals with Parkinson’s disease without cognitive impairment.

Methods

Forty-nine individuals with Parkinson’s disease without cognitive impairment participated in a test-retest reliability study. At two outpatient visits 8 days apart, the participants completed comprehensive questionnaires and single-item questions: International Physical Activity Questionnaire-Short Form (IPAQ-SF), Physical Activity Scale for the Elderly (PASE), Saltin-Grimby Physical Activity Level Scale (SGPALS) and Health on Equal Terms (HOET). Test-retest reliability was evaluated using the intraclass correlation coefficient (ICC), standard error of measurement (SEM), limits of agreement, weighted kappa or the Svensson method.

Results

Several of the physical activity questionnaires had relatively low test-retest reliability, including the comprehensive questionnaires (IPAQ-SF and PASE). Total physical activity according to IPAQ-SF had an ICC value of 0.46 (95% confidence interval [CI], 0.21–0.66) and SEM was 2891 MET-min/week. The PASE total score had an ICC value of 0.66 (95% CI, 0.46–0.79), whereas the SEM was 30 points. The single-item scales of SGPALS-past six months (SGPALS-6 m) and HOET question 1 (HOET-q1) with longer time frames (6 or 12 months, respectively) showed better results. Weighted kappa values were 0.64 (95% CI, 0.45–0.83) for SGPALS-6 m and 0.60 (95% CI, 0.39–0.80) for HOET-q1, whereas the single-item questions with a shorter recall period had kappa values < 0.40.

Conclusions

Single-item questions with a longer time frame (6 or 12 months) for physical activity were shown to be more reliable than multi-item questionnaires such as the IPAQ-SF and PASE in individuals with Parkinson’s disease without cognitive impairments. There is a need to develop a core outcome set to measure physical activity in people with Parkinson’s disease, and there might be a need to develop new physical activity questionnaires.
Genetic and treatment profiles of patients with concurrent Epidermal Growth Factor Receptor (EGFR) and Anaplastic Lymphoma Kinase (ALK) mutations
Authors: Yang Xiaodan , Zhong Jia , Yu Zhuo , Zhuo Minglei , Zhang Min , Chen Rongrong , Xia Xuefeng , Zhao Jun
Published: October 2021

Background

EGFR and ALK alternations often contribute to human malignancies, including lung cancer. EGFR and ALK mutations are usually sensitive to EGFR-tyrosine kinase inhibitors (TKIs) and ALK-TKIs. Although generally mutually exclusive, these mutations do co-exist in rare cases. This study investigated the frequencies, clinical characteristics, therapeutic efficacies, and genetic profiles of lung cancer patients with EGFR and ALK co-mutations.

Methods

Patients with concurrent EGFR and ALK mutations were included in this study, which analyzed mutation profiles and treatment histories. SPSS20.0 were used for survival analysis.

Results

Among 271 ALK-positive (ALK-pos) and 2975 EGFR-positive (EGFR-pos) patients in our database, nine (2.6% of ALK-pos and 0.2% of EGFR-pos) patients had concurrent EGFR and ALK mutations (including three exon19 Indel + EML4-ALK, two exon19 Indel + STRN-ALK, two L858R + L1152R, one L858R + EML4-ALK, and one G719C + S768I + STRN-ALK). Eight patients had at least one type of EGFR-TKIs treatment. The median progression free survival (PFS) of these patients on first-generation EGFR-TKIs was 14.5 months (95% CI: 11 - NR). Of these eight patients, one who progressed on Gefitinib and subsequently on Osimertinib had a T790M + C797G. The other seven EGFR-TKIs resistance patients had no known resistance mutations. No patients had ALK mutations before treatment, so ALK mutations may have developed as resistance mechanisms during EGFR-TKIs therapies. EGFR-TKIs-treated patients with EGFR/ALK L1152R mutations generally had a shorter PFS than patients with other mutation combinations.

Conclusions

ALK and EGFR mutations coincide at a relatively low frequency in lung cancer patients. ALK mutations developed either synchronously or heterochronously with EGFR mutations. Two ALK mutations (L1152R and STRN-ALK) may co-exist with EGFR mutations at a higher frequency than others. Most EGFR/ALK co-alteration patients (other than the EGFR/ALK L1152R type) can benefit from first line EGFR-TKIs.