bluuebunny/crossref_metadata_2025_split huggingface dataset:
The burden of depressive disorders in musculoskeletal diseases: is there an association between mood and inflammation?
Authors: Chimenti Maria Sole , Fonti Giulia Lavinia , Conigliaro Paola , Triggianese Paola , Bianciardi Emanuela , Coviello Marialuce , Lombardozzi Ginevra , Tarantino Giulia , Niolu Cinzia , Siracusano Alberto , Perricone Roberto 
Published: January 2021

Abstract
Importance
Evidence emerged concerning how inflammatory arthritis and mood disorders can often occur in the same patient and show a similar clinical pattern. An overview of the rheumatological and psychiatric aspects of these diseases can certainly be useful for the improvement of patients' clinical and therapeutic management.

Objective
The aim of this narrative review was to summarize existing literature about common pathogenetic and clinical aspects as a means of improving management and therapeutic approach in patients affected by rheumatoid arthritis, psoriatic arthritis and spondyloarthritis. Outcomes such as disease activity indexes and patient reported outcomes (PROs) were considered.

Findings
Common pathogenetic pathways emerged between inflammatory arthritis and mood disorders. Pro-inflammatory mechanisms, such as TNFα, IL-6, IL-17 and oxidative stress factors as well as neurotransmitter alterations at the level of CNS and blood–brain barrier (BBB) cells are involved. The activation of these common pathogenetic pathways is, also, affected by the same triggers, such as smoking, stress, lifestyle, and evidence has emerged concerning the possibility of the clinical efficacy of using the same therapeutic approaches.

Conclusions
The main causes of the variability in clinical studies outcomes are the rheumatological diseases considered, the prevalence of depression in the general population and in patients with rheumatological diseases and the type of depressive symptom examined. Patients affected by inflammatory arthritis can present symptoms and signs in common with mood disorders, leading to possible clinical overlap. There are still few studies analyzing this concept: they are extremely heterogeneous, both in the characteristics of the population taken into consideration and in the methods used for the definition of depressive disorder, but the suggestions of the data obtained so far are promising and deserve to be pursued.
Participatory analysis of groundnut (Arachis hypogaea L.) cropping system and production constraints in Burkina Faso
Authors: Sinare Boubacar , Miningou Amos , Nebié Baloua , Eleblu John , Kwadwo Ofori , Traoré Appolinaire , Zagre Bertin , Desmae Haile 
Published: January 2021

AbstractBackgroundGroundnut is one of the major legume crops grown as food and cash crop across the different agroecological zones of Burkina Faso. It is ranked the 2nd important legume crop for household food, nutrition, and income generation for both rural and urban zones, contributing significantly to food supply and economy of the country. Despite its importance and breeding efforts to develop improved varieties, groundnut productivity remains low. Assessing and describing the present groundnut cropping system and production constraints as well as gender dynamics in the main production areas will help in defining the groundnut breeding priorities.MethodsA participatory rural appraisal study was conducted in three groundnut production regions (central-eastern, central-northern, and central-western). In each region, 4 villages were selected with a total of 124 farmers interviewed to collect data on socio-demographics, farming systems, cropping practices, and production constraints. Data analysis was carried out for qualitative and quantitative variables using STATA 14. Analysis of variance was conducted across regions and gender, and also between and within regions. Kendall’s coefficients were determined for qualitative variables across regions for the constraints using the pairwise rank. Pearson’s correlation was carried out to assess the relationship between variables, and the chi-square test was used to assess the difference in farmer preferences.ResultsThe study revealed a cropping system of groundnut in an environment largely affected by climate change and in a subsistence and extensive agriculture. There is a variation in the groundnut cropping system across the regions. Gender plays a key role in the production of the groundnut, and 48.39% of women are engaged in groundnut cropping with less access to land and production resources. A yield gap between men and women was observed with men achieving more yield than women. There was a strong correlation between the use of improved varieties and technical assistance. A strong correlation was observed between farm size and production, and farm size and sex denoting an extensive production. Production constraints, although similar, were perceived and ranked differently between regions. The lack of improved varieties, absence of agricultural credit, lack of production tools, the high price of seeds, the high price of fertilizer, drought, and disease are some of the important constraints affecting groundnut productivity.ConclusionThis study provides a recent view of groundnut cropping, allowing a good understanding of the farmers’ situation. The result will contribute to the refining of breeding priorities and guide further activities in groundnut breeding in Burkina Faso.
Various forms of alcohol use and their predictors among pregnant women in post conflict northern Uganda: a cross sectional study
Authors: Agiresaasi Apophia , Nassanga Goretti , Maina Gakenia Wamuyu , Kiguli Juliet , Nabiwemba Elizabeth , Tumwesigye Nazarius Mbona 
Published: January 2021

AbstractBackgroundAlcohol use during pregnancy has been associated with several births and developmental disorders. This study set out to determine the various forms of alcohol consumption among pregnant women and their predictors in post conflict Northern Uganda.MethodsIn the months of May to June 2019, we conducted a cross sectional study among 420 pregnant women seeking antenatal care services at both Government and private health facilities in Gulu, Kitgum and Pader districts in Northern Uganda. We asked them about consumption of various alcoholic beverages. A three stage stratified cluster sampling approach was used and study participants randomly selected from health facilities of interest. We used descriptive statistics to estimate the prevalence of various forms of alcohol use. The chi- square test and logistic regression were used to assess associations of alcohol use among respondents and their socio - demographic and other characteristics.ResultsOverall 99 women (23.6%) reported current alcohol use (any amount). Up to 11% (N = 11) of all drinkers were identified by the AUDIT to be women with problem drinking behavior, 8% (N = 8) of women reported hazardous drinking and only four (4%) were women with active alcohol dependent behavior. Predictors of maternal alcohol use included pre-pregnancy alcohol consumption, knowledge, attitude, education level, parity and residence.ConclusionsThis study indicates that alcohol use (any mount) during pregnancy is high while alcohol dependence, problematic and hazardous drinking is low. Knowledge and attitude were important predictors of alcohol use. While alleviating alcohol use, development partners and relevant government departments should consider communication and other interventions that increase knowledge and risk perception on maternal drinking. Other risk factors that predict maternal drinking such as prior alcohol use, residence and parity should be mitigated or eliminated.
How the pan-genome is changing crop genomics and improvement
Authors: Della Coletta Rafael , Qiu Yinjie , Ou Shujun , Hufford Matthew B. , Hirsch Candice N. 
Published: January 2021

AbstractCrop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to facilitate crop improvement. The study of structural variation within species and the characterization of the pan-genome has revealed extensive genome content variation among individuals within a species that is paradigm shifting to crop genomics and improvement. Here, we review advances in crop genomics and how utilization of these tools is shifting in light of pan-genomes that are becoming available for many crop species.
SpRY greatly expands the genome editing scope in rice with highly flexible PAM recognition
Authors: Xu Ziyan , Kuang Yongjie , Ren Bin , Yan Daqi , Yan Fang , Spetz Carl , Sun Wenxian , Wang Guirong , Zhou Xueping , Zhou Huanbin 
Published: January 2021

Abstract
Background
Plant genome engineering mediated by various CRISPR-based tools requires specific protospacer adjacent motifs (PAMs), such as the well-performed NGG, NG, and NNG, to initiate target recognition, which notably restricts the editable range of the plant genome.

Results
In this study, we thoroughly investigate the nuclease activity and the PAM preference of two structurally engineered SpCas9 variants, SpG and SpRY, in transgenic rice. Our study shows that SpG nuclease favors NGD PAMs, albeit less efficiently than the previously described SpCas9-NG, and that SpRY nuclease achieves efficient editing across a wide range of genomic loci, exhibiting a preference of NGD as well as NAN PAMs. Furthermore, SpRY-fused cytidine deaminase hAID*Δ and adenosine deaminase TadA8e are generated, respectively. These constructs efficiently induce C-to-T and A-to-G conversions in the target genes toward various non-canonical PAMs, including non-G PAMs. Remarkably, high-frequency self-editing events (indels and DNA fragments deletion) in the integrated T-DNA fragments as a result of the nuclease activity of SpRY are observed, whereas the self-editing of SpRY nickase-mediated base editor is quite low in transgenic rice lines.

Conclusions
The broad PAM compatibility of SpRY greatly expands the targeting scope of CRISPR-based tools in plant genome engineering.
Unraveling city-specific signature and identifying sample origin locations for the data from CAMDA MetaSUB challenge
Authors: Zhang Runzhi , Walker Alejandro R. , Datta Susmita 
Published: January 2021

AbstractBackgroundComposition of microbial communities can be location-specific, and the different abundance of taxon within location could help us to unravel city-specific signature and predict the sample origin locations accurately. In this study, the whole genome shotgun (WGS) metagenomics data from samples across 16 cities around the world and samples from another 8 cities were provided as the main and mystery datasets respectively as the part of the CAMDA 2019 MetaSUB “Forensic Challenge”. The feature selecting, normalization, three methods of machine learning, PCoA (Principal Coordinates Analysis) and ANCOM (Analysis of composition of microbiomes) were conducted for both the main and mystery datasets.ResultsFeatures selecting, combined with the machines learning methods, revealed that the combination of the common features was effective for predicting the origin of the samples. The average error rates of 11.93 and 30.37% of three machine learning methods were obtained for main and mystery datasets respectively. Using the samples from main dataset to predict the labels of samples from mystery dataset, nearly 89.98% of the test samples could be correctly labeled as “mystery” samples. PCoA showed that nearly 60% of the total variability of the data could be explained by the first two PCoA axes. Although many cities overlapped, the separation of some cities was found in PCoA. The results of ANCOM, combined with importance score from the Random Forest, indicated that the common “family”, “order” of the main-dataset and the common “order” of the mystery dataset provided the most efficient information for prediction respectively.ConclusionsThe results of the classification suggested that the composition of the microbiomes was distinctive across the cities, which could be used to identify the sample origins. This was also supported by the results from ANCOM and importance score from the RF. In addition, the accuracy of the prediction could be improved by more samples and better sequencing depth.
Significance of serum branched-chain amino acid to tyrosine ratio measurement in athletes with high skeletal muscle mass
Authors: Tsunekawa Katsuhiko , Matsumoto Ryutaro , Ushiki Kazumi , Martha Larasati , Shoho Yoshifumi , Yanagawa Yoshimaro , Ishigaki Hirotaka , Yoshida Akihiro , Araki Osamu , Nakajima Kiyomi , Kimura Takao , Murakami Masami 
Published: January 2021

Abstract
Background
Few nutritional markers reflect the hypermetabolic state of athletes with high levels of skeletal muscle. Although branched-chain amino acids (BCAA) play crucial roles in protein metabolism in skeletal muscle, the relationship between skeletal muscle mass and amino acid imbalances caused by the metabolism of BCAA and aromatic amino acids remains unclear. The aim of this study is to test the hypothesis that athletes with high levels of skeletal muscle mass have plasma amino acid imbalances, assessed by serum BCAA to tyrosine ratio (BTR) which can be measured conveniently.

Methods
The study enrolled 111 young Japanese men: 70 wrestling athletes and 41 controls. None of them were under any medications, extreme dietary restrictions or intense exercise regimens. Each participant’s body composition, serum concentrations of albumin and rapid turnover proteins including transthyretin and transferrin, BTR, and thyroid function were assessed.

Results
Compared to the controls, the athletes had significantly higher skeletal muscle index (SMI) (p < 0.001), and lower serum albumin concentration (p < 0.001) and BTR (p < 0.001). Kruskal–Wallis tests showed that serum albumin concentration and BTR were significantly lower in the participants with higher SMI. Serum albumin concentration and BTR were inversely correlated with SMI by multiple regression analysis (logarithmic albumin, β = − 0.358, p < 0.001; BTR, β = − 0.299, p = 0.001). SMI was inversely and transthyretin was positively correlated with serum albumin (SMI, β = − 0.554, p < 0.001; transthyretin, β = 0.379, p < 0.001). Serum concentration of free 3,5,3′-triiodothyronine (FT3) was inversely correlated with BTR, and, along with SMI and albumin, was independent predictor of BTR (SMI, β = − 0.321, p < 0.001; FT3, β = − 0.253, p = 0.001; logarithmic albumin, β = 0.261, p = 0.003). However, FT3 was not correlated with SMI or serum albumin. Serum concentrations of rapid turnover proteins were not correlated with BTR.

Conclusions
Increased skeletal muscle mass enhances the circulating amino acid imbalances, and is independently facilitated by thyroid hormones. Serum BTR may be a useful biomarker to assess the hypermetabolic state of wrestling athletes with high levels of skeletal muscle.
The degree of microsatellite instability predicts response to PD-1 blockade immunotherapy in mismatch repair-deficient/microsatellite instability-high colorectal cancers
Authors: Wang Qiao-Xuan , Qu Chun-Hua , Gao Yuan-Hong , Ding Pei-Rong , Yun Jing-Ping , Xie Dan , Cai Mu-Yan 
Published: January 2021

AbstractThe development of programmed cell death-1 inhibitor (PD-1) has shed light on the treatment of tumors with deficiencies in DNA mismatch repair system or microsatellite instability (dMMR/MSI). However, predicting the subset in this group that will benefit from PD-1 blockade remains a challenge. In this study, we aimed to investigate the relationship between the degree of microsatellite instability and the responses to anti-PD-1 immunotherapy. 33 patients with colorectal adenocarcinoma who had a known MSI status and received anti-PD-1 immunotherapy were included. PCR results for MSI of the whole cohort were collected and treatment response was evaluated. Our data indicated that objective response rate (ORR) in instability-high group (instability loci ≥ 3) was significantly higher than ORR in instability-intermediate group (13/16 versus 6/17, P = 0.008). Besides, patients in instability-high group had significant longer progression-free survival (log-rank test, P = 0.004), and a significant increase in T lymphocyte infiltration and cytolytic activity in tumors. Future study might implement the intensity of microsatellite instability for more delicate selection for anti-PD-1 therapy in patient with dMMR/MSI-H tumors.
Has Bipolar Disorder become a predominantly female gender related condition? Analysis of recently published large sample studies
Authors: Dell’Osso Bernardo , Cafaro Rita , Ketter Terence A. 
Published: January 2021

AbstractBipolar Disorders (BD) are disabling and severe psychiatric disorders, commonly perceived as equally affecting both men and women. The prevalence of BD in the general population has been growing over the last decade, however, few epidemiological studies are available regarding BD gender distribution, leaving unanswered the question whether the often reported increment of BD diagnosis could be gender specific. In fact, BD in female patients can often be misdiagnosed as MDD, leaving such women non correctly treated for longer times than their male counterparts. From this perspective, we searched literature for large sample (> 1000 subjects) studies published in the last decade (2010 onward) on BD patients. We included ten large sample studies that reported the gender distribution of their samples, and we therefore analysed them. Our results show a higher preponderance of female patients in every sample and sub-sample of BDI and BDII, supporting our hypothesis of an increase in BD diagnosis in females. BD in women presents with higher rates of rapid cycling, depressive polarity and suicide attempts, characteristics of non inferior severity compared to males; prompt recognition and adequate treatment of BD is therefore crucial to reduce risks and improve quality of life of affected women. In this regard, our results could lead the way for national or international epidemiological studies with the aim of more accurately assessing gender-specific prevalence of BD.
Process data, the new frontier for assessment development: rich new soil or a quixotic quest?
Authors: Provasnik Stephen 
Published: January 2021

AbstractThis paper presents the concepts and observations in the author’s keynote address at the May 2019 “Opportunity versus Challenge: Exploring Usage of Log-File and Process Data in International Large-Scale Assessments” conference in Dublin, Ireland. This paper recaps briefly some key points that emerged at the December 2018 ETS symposium on process data in Washington, DC, and suggests some common terminology and concepts for facilitating future meaningful discussion. It then borrows some concepts from evolutionary biologists to take a critical look at process data and some of its ethical implications before turning to discuss major applications for and challenges of using process data and logfiles. The second half of this paper then maps out the terrain in which process data emerges as a “byproduct” of the shift from paper-and-pencil testing to digital-based assessments (DBA) and looks closely at how process data interacts with the development and operationalization of assessment systems. This interaction suggests new, fresh ways of improving national and international assessment system processes, and ultimately the measurement of cognitive skills, while venturing into the new frontiers opened with process data.
A patient-specific 3D model of the knee to compare the femoral rollback before and after total knee arthroplasty (TKA)
Authors: Mercader Alexandra , Röttinger Timon , Bigdeli Amir , Lüth Tim C. , Röttinger Heinz 
Published: January 2021

Abstract
Purpose
Total knee arthroplasty (TKA) is nowadays performed as a standard procedure on a large number of patients suffering from arthrosis. Replacing the knee joint causes changes in the geometry and kinematics of the knee, which are unique to each individual. This research focuses on the method to detect these changes after TKA and on the impact on the knee movement. This approach could reduce complications in patients with post-operative pain and reduce the number of revisions.

Methods
A 3D model of a patient’s knee was made by measuring the movement with a medically certified infrared stereo camera. This measurement was combined with the 3D model of the patient’s bones, previously segmented from the CT scan. This model is printed in 3D, one part being the mechanism that follows the movement of the patient, and the other part being the 3D copy of the femur and tibia bones. The knee replacement operation is performed directly on the model and the resulting rollback is being measured before and after TKA.

Results
We observe a difference in the rollback before and after TKA on the 3D printed model. The variation in size and shape of the femoral implant compared to the natural femur condyles is one of the reasons for the changes in the rollback effect. The rollback is half as large after the prosthesis insertion, which confirms the fact that the femoral prosthesis geometry influences the knee kinematics.

Conclusions
In this study, a first 3D model combining the patient-specific kinematic and the geometry of his bones has been constructed. This model allows the surgeon to validate the plan of the operation, but also to understand the problems and consequences generated by the prosthesis insertion. The rollback is one of the most important motion of the knee joint and this behavior could be quantified, providing comparative analysis of the knee joint before and after the operation. As a future study, the model could be used to analyse more parameters of the TKA such as the impact of different implantation methods.
Application of an economic calculator to determine the cost of porcine reproductive and respiratory syndrome at farm-level in 21 pig herds in Germany
Authors: Renken C. , Nathues C. , Swam H. , Fiebig K. , Weiss C. , Eddicks M. , Ritzmann M. , Nathues H. 
Published: January 2021

AbstractBackgroundPorcine Reproductive and Respiratory Syndrome Virus (PRRSV) continues to be a major economic issue for the swine industry worldwide, not only due to acute outbreaks but also endemic infections. PRRS disease severity and consequently financial losses can vary greatly between endemically infected farms and estimation of damage is challenging. This study aimed to assess the economic effect of PRRS in a systematic way at individual farm-level for endemically infected herds, using a PRRS cost simulation tool. In total 21 German sow herds with endemic PRRSV infection were investigated. Data on health and production performance, farm management and environment to be fed into the calculator was collected on each farm, and blood samples taken to confirm the PRRSV status.ResultsAll study farms experienced a significant loss attributable to PRRS. The median farm budget across all farms was − 31 € per sow and year, compared to a median simulated farm budget of 248 € if these farms had been PRRSV negative. The median total loss attributable to PRRS was 74,181 € per farm per year, corresponding to a median total loss per sow and year of 255 €. The impact of PRRS on farm profits was − 19.1% on average and − 41% in the worst case.ConclusionsThe calculated losses give a good hint of the economic damage due to PRRS for the pig industry. Even in endemically infected farms, farmers face a non-negligible damage and profit from a concerted PRRS control. The calculator has proven itself in the field to render a valid estimation of losses due to PRRS in endemically infected farms.