bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Role of Patients’ Psychological Comfort in Optimizing Indoor Healing Environments: A Case Study of the Indoor Environments of Recently Built Hospitals in Sulaimani City, Kurdistan, Iraq
Authors: Mahmood Fouad Jalal , Tayib Abdullah Yusif 
Published: December 2019

Objective: This study investigates how patients and medical staff assess the physical environments of two recently built hospitals in Sulaimani City to understand the extent to which indoor environmental factors influence the creation of an optimal healing environment. Background: A contemporary healing environment may be recognized by the quality of an indoor environment in positively influencing patients’ psychological comfort and supporting their recovery. Method: Post-occupancy evaluations were conducted in Shar General Hospital and Faruk Medical City wards. A 43-item questionnaire was distributed to 312 patients, doctors, and nurses to gather their perspectives. In total, 175 valid questionnaires were retrieved. Results: The results show that the quality of the indoor environments met patients’ psychological needs and expectations, and as a result, they were generally satisfied with the indoor healing environments. The findings from the patient and medical staff surveys suggest three essential factors in creating a healing environment, which are (1) Interior appearance, (2) Privacy, and (3) Comfort and control. Significant negative correlations of some demographic characteristics, such as educational attainment and age, with patient satisfaction were observed. Conclusions: This study shows that exploring patients’ and medical staff’s experiences can reveal factors that positively influence patients’ satisfaction levels, which may vary depending on their sociocultural perspectives and personal characteristics. Additionally, the findings emphasize the role of the tested factors in increasing patients’ satisfaction levels, optimizing healing environments, and informing design decisions.
Digital interventions for people living with non-communicable diseases in India: A systematic review of intervention studies and recommendations for future research and development
Authors: Hossain Md Mahbub , Tasnim Samia , Sharma Rachit , Sultana Abida , Shaik Araish Farzana , Faizah Farah , Kaur Ravneet , Uppuluri Madhuri , Sribhashyam Mitali , Bhattacharya Sudip 
Published: December 2019

Background A high burden of non-communicable diseases (NCDs) is contributing to high mortality and morbidity in India. Recent advancements in digital health interventions, including mHealth, eHealth, and telemedicine, have facilitated patient-centered care for NCDs. Objective This systematic review aims to evaluate the current evidence on digital interventions for people living with NCDs in India and the outcomes of those interventions. Methods We adopted PRISMA guidelines and systematically reviewed articles from MEDLINE, CINAHL, PsycINFO, ERIC, and Scopus databases with following criteria: journal articles presenting digital intervention(s) used by people with at least one of the NCDs, reporting health outcomes following the intervention, studies conducted in India among Indian population. Results Among 1669 articles retrieved from multiple sources, only 13 articles met our criteria. Most ( n = 7) studies were conducted in southern states of India; eight studies included patients with diabetes, followed by neuropsychiatric disorders and other NCDs. Five studies recruited participants from tertiary hospitals; six interventions used text-messaging for delivering health services, and 10 studies reported randomized controlled trials. All the studies reported positive health outcomes following the intervention, including better self-management, increased patient–provider communication, improved medication adherence, and reduced disease symptoms. Most studies scored moderate to high in quality assessment checklist of Downs and Black. Conclusion Current evidence suggests a low number of interventions with positive outcomes. Future research should explore avenues of advanced technologies ensuring equitable and sustainable development of digital health interventions for people living with NCDs in India.
PARP-1 deregulation in multiple sclerosis
Authors: Meira Maria , Sievers Claudia , Hoffmann Francine , Bodmer Heidi , Derfuss Tobias , Kuhle Jens , Haghikia Aiden , Kappos Ludwig , Lindberg Raija LP 
Published: December 2019

Background Poly (ADP-ribose) polymerase 1 (PARP-1) plays pivotal roles in immune and inflammatory responses. Accumulating evidence suggests PARP-1 as a promising target for immunomodulation in multiple sclerosis and natalizumab-associated progressive multifocal leukoencephalopathy. Objective This study explores expression of PARP-1 and downstream effectors in multiple sclerosis and during natalizumab treatment. Methods Transcriptional expressions were studied by real-time reverse transcriptase polymerase chain reaction on CD4+T/CD8+T/CD14+/B cells and peripheral blood mononuclear cells from healthy volunteers, untreated and natalizumab-treated non-progressive multifocal leukoencephalopathy and progressive multifocal leukoencephalopathy multiple sclerosis patients. Results PARP-1 expression was higher in CD4+T, CD8+T and B cells from untreated patients compared to healthy volunteers. Natalizumab treatment restored deregulated PARP-1 expression in T cells but not in B cells. Sustained upregulation of PARP-1 was associated with decreased expression of downstream PARP-1 factors such as TGFBR1/TGFBR2/BCL6 in B cells. Notably, a higher expression of PARP-1 was detected in progressive multifocal leukoencephalopathy patients. Conclusions Given the importance of PARP-1 in inflammatory processes, its upregulation in multiple sclerosis lymphocyte populations suggests a potential role in the immune pathogenesis of multiple sclerosis. Strikingly higher PARP-1 expression in progressive multifocal leukoencephalopathy cases suggests its involvement in progressive multifocal leukoencephalopathy disease pathomechanisms. These results further support the value of PARP-1 inhibitors as a potential novel therapeutic strategy for multiple sclerosis and natalizumab-associated progressive multifocal leukoencephalopathy.
Patient-Reported Knee Outcome Scores With Soft Tissue Quadriceps Tendon Autograft Are Similar to Bone–Patellar Tendon–Bone Autograft at Minimum 2-Year Follow-up: A Retrospective Single-Center Cohort Study in Primary Anterior Cruciate Ligament Reconstruction Surgery
Authors: Perez Jose R. , Emerson Christopher P. , Barrera Carlos M. , Greif Dylan N. , Cade William H. , Kaplan Lee D. , Baraga Michael G. 
Published: December 2019

Background: Quadriceps tendon (QT)–bone autografts used during anterior cruciate ligament (ACL) reconstruction have provided comparable outcomes and decreased donor-site morbidity when compared with bone–patellar tendon–bone (BPTB) autografts. No study has directly compared the outcomes of the all–soft tissue QT autograft with that of the BPTB autograft. Hypothesis: Patient-reported knee outcome scores and rates of postoperative complication after primary ACL reconstruction with QT autografts are no different from BPTB autografts at a minimum 2-year follow-up. Study Design: Cohort study; Level of evidence, 3. Methods: A total of 75 patients who underwent primary autograft ACL reconstruction with QT or BPTB autografts between January 1, 2015, and March 31, 2016, at a single hospital center were contacted by telephone and asked to complete the International Knee Documentation Committee (IKDC) Subjective Knee Evaluation, Tegner activity level scale, and Lysholm knee scoring scale. Information about the subsequent surgeries performed on the operative knee was also collected. Statistical analysis was performed using the Kruskal-Wallis test and the Fisher exact test for categorical data. Results: Fifty patients (28 QT, 22 BPTB) completed the surveys at a mean follow-up of 33.04 months (range, 24-44 months). For the QT versus the BPTB group respectively, the median IKDC scores were 94.83 (interquartile range [IQR], 7.61) versus 94.83 (IQR, 10.92) ( P = .47), the median Tegner scores were 6 (IQR, 2.5) versus 6 (IQR, 2.75) ( P = .48), and the median Lysholm scores were 95 (IQR, 9) versus 95 (IQR, 13) ( P = .27). Additionally, 2 QT patients and 3 BPTB patients required follow-up arthroscopy for arthrolysis ( P = .64). There was 1 graft failure in the QT group requiring revision surgery. Conclusion: There was no statistical difference in patient-reported knee outcomes or graft complication rates between the QT and BPTB autograft groups at a minimum 2-year follow-up after primary ACL reconstruction. This study highlights that the all–soft tissue QT autograft may be a suitable graft choice for primary ACL reconstruction.
Deficiency of sphingomyelin synthase 1 but not sphingomyelin synthase 2 reduces bone formation due to impaired osteoblast differentiation
Authors: Matsumoto Goichi , Hashizume Chieko , Watanabe Ken , Taniguchi Makoto , Okazaki Toshiro 
Published: December 2019

AbstractBackgroundThere are two isoforms of sphingomyelin synthase (SMS): SMS1 and SMS2. SMS1 is located in the Golgi apparatus only while SMS2 is located in both the plasma membrane and the Golgi apparatus. SMS1 and SMS2 act similarly to generate sphingomyelin (SM). We have undertaken the experiments reported here on SMS and osteoblast differentiation in order to better understand the role SMS plays in skeletal development.MethodsWe analyzed the phenotype of a conditional knockout mouse, which was generated by mating a Sp7 promoter-driven Cre-expressing mouse with an SMS1-floxed SMS2-deficient mouse (Sp7-Cre;SMS1f/f;SMS2−/−mouse).ResultsWhen we comparedSp7-Cre;SMS1f/f;SMS2−/−mice with C57BL/6, SMS2-deficient mice (SMS1f/f;SMS2−/−) and SP7-Cre positive control mice (Sp7-Cre, Sp7-Cre;SMS1+/+;SMS2+/−andSp7-Cre;SMS1+/+;SMS2−/−), we found that although cartilage formation is normal,Sp7-Cre;SMS1f/f;SMS2−/−mice showed reduced trabecular and cortical bone mass, had lower bone mineral density, and had a slower mineral apposition rate than control mice. Next, we have used a tamoxifen-inducible knockout system in vitro to show that SMS1 plays an important role in osteoblast differentiation. We cultured osteoblasts derived fromERT2-Cre;SMS1f/fSMS2−/−mice. We observed impaired differentiation of these cells in response to Smad1/5/8 and p38 that were induced by bone morphogenic protein 2 (BMP2). However, Erk1/2 phosphorylation was unaffected by inactivation of SMS1.ConclusionsThese findings provide the first genetic evidence that SMS1 plays a role in bone development by regulating osteoblast development in cooperation with BMP2 signaling. Thus, SMS1 acts as an endogenous signaling component necessary for bone formation.
The importance of the rate of pure “attended deaths at home” for objective outcome indicator for assessing the prevalence of home care in Japan
Authors: Kakiuchi Yasuhiro , Nagao Ryoko , Ochiai Eriko , Kakimoto Yu , Osawa Motoki 
Published: December 2019

Abstract
Background
No study has yet been performed on the importance of the rate of pure “attended deaths at home,” excluding examined deaths subjected to a postmortem examination. Therefore, in the present study, we investigated actual state of pure “attended deaths at home,” in order to provide reference data for the future development of end-of-life care at home.

Methods
We performed a detailed survey in Yokohama City according to the type of death, age, and underlying cause of death in cases of home deaths, based on the detailed version of the Vital Statistics Survey Death Forms. Then, we divided deaths occurring in each municipality in Kanagawa Prefecture into two categories: “examined deaths” or “attended deaths,” which were also stratified by the place of death, based on the Vital Statistics, and data on number of death cases subjected to postmortem examination from the Kanagawa Prefectural Police Headquarters.

Results
In 2013, the survey in Yokohama City showed large differences in age distribution and cause of death between examined and attended deaths. In 2014, home deaths accounted for 15.7% of all deaths in the prefecture, whereas the overall proportion of attended deaths at home was 6.9%.

Conclusions
We should utilize the rate of pure “attended deaths at home” for objective outcome indicator.
Subsidising urban and sub-urban transport – distributional impacts
Authors: Fearnley Nils , Aarhaug Jørgen 
Published: December 2019

AbstractBackground and methodsThis paper studies distributional effects of public transport (PT) subsidies focusing on the Greater Oslo region. We identify how different PT markets enjoy different levels of subsidies. We describe how subsidies are distributed along PT modes and their respective patronage. This is done by document studies and travel surveys, supplemented by expert inquiries.ResultsWe find that high-income groups, served by regional trains and high-speed crafts, receive large per passenger and per passenger-kilometre subsidy, while lower-income areas, typically served by local and regional buses, metros and local trains, receive lower subsidies per passenger. Peak traffic receives higher subsidies than off-peak traffic. The overall distributional profile is, however, found to be moderately progressive, in particular because of the socio-economic profile of the average PT passenger relative to the population as a whole.
Level-biases in estimated breeding values due to the use of different SNP panels over time in ssGBLUP
Authors: Nordbø Øyvind , Gjuvsland Arne B. , Eikje Leiv Sigbjørn , Meuwissen Theo 
Published: December 2019

AbstractBackgroundThe main aim of single-step genomic predictions was to facilitate optimal selection in populations consisting of both genotyped and non-genotyped individuals. However, in spite of intensive research, biases still occur, which make it difficult to perform optimal selection across groups of animals. The objective of this study was to investigate whether incomplete genotype datasets with errors could be a potential source of level-bias between genotyped and non-genotyped animals and between animals genotyped on different single nucleotide polymorphism (SNP) panels in single-step genomic predictions.ResultsIncomplete and erroneous genotypes of young animals caused biases in breeding values between groups of animals. Systematic noise or missing data for less than 1% of the SNPs in the genotype data had substantial effects on the differences in breeding values between genotyped and non-genotyped animals, and between animals genotyped on different chips. The breeding values of young genotyped individuals were biased upward, and the magnitude was up to 0.8 genetic standard deviations, compared with breeding values of non-genotyped individuals. Similarly, the magnitude of a small value added to the diagonal of the genomic relationship matrix affected the level of average breeding values between groups of genotyped and non-genotyped animals. Cross-validation accuracies and regression coefficients were not sensitive to these factors.ConclusionsBecause, historically, different SNP chips have been used for genotyping different parts of a population, fine-tuning of imputation within and across SNP chips and handling of missing genotypes are crucial for reducing bias. Although all the SNPs used for estimating breeding values are present on the chip used for genotyping young animals, incompleteness and some genotype errors might lead to level-biases in breeding values.
Base-pair ambiguity and the kinetics of RNA folding
Authors: Zhou Guangyao , Loper Jackson , Geman Stuart 
Published: December 2019

Abstract
Background
A folding RNA molecule encounters multiple opportunities to form non-native yet energetically favorable pairings of nucleotide sequences. Given this forbidding free-energy landscape, mechanisms have evolved that contribute to a directed and efficient folding process, including catalytic proteins and error-detecting chaperones. Among structural RNA molecules we make a distinction between “bound” molecules, which are active as part of ribonucleoprotein (RNP) complexes, and “unbound,” with physiological functions performed without necessarily being bound in RNP complexes. We hypothesized that unbound molecules, lacking the partnering structure of a protein, would be more vulnerable than bound molecules to kinetic traps that compete with native stem structures. We defined an “ambiguity index”—a normalized function of the primary and secondary structure of an individual molecule that measures the number of kinetic traps available to nucleotide sequences that are paired in the native structure, presuming that unbound molecules would have lower indexes. The ambiguity index depends on the purported secondary structure, and was computed under both the comparative (“gold standard”) and an equilibrium-based prediction which approximates the minimum free energy (MFE) structure. Arguing that kinetically accessible metastable structures might be more biologically relevant than thermodynamic equilibrium structures, we also hypothesized that MFE-derived ambiguities would be less effective in separating bound and unbound molecules.

Results
We have introduced an intuitive and easily computed function of primary and secondary structures that measures the availability of complementary sequences that could disrupt the formation of native stems on a given molecule—an ambiguity index. Using comparative secondary structures, the ambiguity index is systematically smaller among unbound than bound molecules, as expected. Furthermore, the effect is lost when the presumably more accurate comparative structure is replaced instead by the MFE structure.

Conclusions
A statistical analysis of the relationship between the primary and secondary structures of non-coding RNA molecules suggests that stem-disrupting kinetic traps are substantially less prevalent in molecules not participating in RNP complexes. In that this distinction is apparent under the comparative but not the MFE secondary structure, the results highlight a possible deficiency in structure predictions when based upon assumptions of thermodynamic equilibrium.
Convergent degeneration of olfactory receptor gene repertoires in marine mammals
Authors: Liu Ake , He Funan , Shen Libing , Liu Ruixiang , Wang Zhijun , Zhou Jingqi 
Published: December 2019

AbstractBackgroundOlfactory receptors (ORs) can bind odor molecules and play a crucial role in odor sensation. Due to the frequent gains and losses of genes during evolution, the number of OR members varies greatly among different species. However, whether the extent of gene gains/losses varies between marine mammals and related terrestrial mammals has not been clarified, and the factors that might underlie these variations are unknown.ResultsTo address these questions, we identified more than 10,000 members of the OR family in 23 mammals and classified them into 830 orthologous gene groups (OGGs) and 281 singletons. Significant differences occurred in the number of OR repertoires and OGGs among different species. We found that all marine mammals had fewer OR genes than their related terrestrial lineages, with the fewest OR genes found in cetaceans, which may be closely related to olfactory degradation. ORs with more gene duplications or loss events tended to be under weaker purifying selection. The average gain and loss rates of OR genes in terrestrial mammals were higher than those of mammalian gene families, while the average gain and loss rates of OR genes in marine mammals were significantly lower and much higher than those of mammalian gene families, respectively. Additionally, we failed to detect any one-to-one orthologous genes in the focal species, suggesting that OR genes are not well conserved among marine mammals.ConclusionsMarine mammals have experienced large numbers of OR gene losses compared with their related terrestrial lineages, which may result from the frequent birth-and-death evolution under varied functional constrains. Due to their independent degeneration, OR genes present in each lineage are not well conserved among marine mammals. Our study provides a basis for future research on the olfactory receptor function in mammals from the perspective of evolutionary trajectories.
Transcriptome analysis reveals plasticity in gene regulation due to environmental cues in Primula sikkimensis, a high altitude plant species
Authors: Gurung Priya Darshini , Upadhyay Atul Kumar , Bhardwaj Pardeep Kumar , Sowdhamini Ramanathan , Ramakrishnan Uma 
Published: December 2019

Abstract
Background
Studying plasticity in gene expression in natural systems is crucial, for predicting and managing the effects of climate change on plant species. To understand the contribution of gene expression level variations to abiotic stress compensation in a Himalaya plant (Primula sikkimensis), we carried out a transplant experiment within (Ambient), and beyond (Below Ambient and Above Ambient) the altitudinal range limit of species. We sequenced nine transcriptomes (three each from each altitudinal range condition) using Illumina sequencing technology. We compared the fitness variation of transplants among three transplant conditions.

Results
A large number of significantly differentially expressed genes (DEGs) between below ambient versus ambient (109) and above ambient versus ambient (85) were identified. Transcripts involved in plant growth and development were mostly up-regulated in below ambient conditions. Transcripts involved in signalling, defence, and membrane transport were mostly up-regulated in above ambient condition. Pathway analysis revealed that most of the genes involved in metabolic processes, secondary metabolism, and flavonoid biosynthesis were differentially expressed in below ambient conditions, whereas most of the genes involved in photosynthesis and plant hormone signalling were differentially expressed in above ambient conditions. In addition, we observed higher reproductive fitness in transplant individuals at below ambient condition compared to above ambient conditions; contrary to what we expect from the cold adaptive P. sikkimensis plants.

Conclusions
We reveal P. sikkimensis’s capacity for rapid adaptation to climate change through transcriptome variation, which may facilitate the phenotypic plasticity observed in morphological and life history traits. The genes and pathways identified provide a genetic resource for understanding the temperature stress (both the hot and cold stress) tolerance mechanism of P. sikkimensis in their natural environment.