bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing Head Impact Exposure in Men and Women During Boxing and Mixed Martial Arts
Authors: Jansen A. Elizabeth , McGrath Morgan , Samorezov Sergey , Johnston Joshua , Bartsch Adam , Alberts Jay 
Published: December 2021

Background: The accumulation of subconcussive impacts has been implicated in permanent neurological impairment. A gap in understanding the relationship between head impacts and neurological function is the lack of precise characterization and quantification of forces that individuals experience during sports training and competition. Purpose: To characterize impact exposure during training and competition among male and female athletes participating in boxing and mixed martial arts (MMA) via an instrumented custom-fit Impact Monitoring Mouthguard (IMM). Study Design: Cross-sectional study; Level of evidence, 3. Methods: Twenty-three athletes (n = 4 women) were provided a custom-fit IMM. The IMM monitored impacts during sparring and competition. All training and competition sessions were videotaped. Video and IMM data were synchronized for post hoc data verification of true positives and substantiation of impact location. IMM data were collected from boxing and MMA athletes at a collaborating site. For each true-positive impact, peak linear acceleration and peak angular acceleration were calculated. Wilcoxon rank sum tests were used to evaluate potential differences in sport, activity type, and sex with respect to each outcome. Differences in impact location were assessed via Kruskal-Wallis tests. Results: IMM data were collected from 53 amateur training sessions and 6 competitions (session range, 5-20 minutes). A total of 896 head impacts (men, n = 786; women, n = 110) were identified using IMM data and video verification: 827 in practice and 69 during competition. MMA and boxers experienced a comparable number of impacts per practice session or competition. In general, MMA impacts produced significantly higher peak angular acceleration than did boxing impacts ( P < .001) and were more varied in impact location on the head during competitions. In terms of sex, men experienced a greater number of impacts than women per practice session. However, there was no significant difference between men and women in terms of impact magnitude. Conclusion: Characteristic profiles of head impact exposure differed between boxing and MMA athletes; however, the impact magnitudes were not significantly different for male and female athletes.
Optimal dimensionality selection for independent component analysis of transcriptomic data
Authors: McConn John Luke , Lamoureux Cameron R. , Poudel Saugat , Palsson Bernhard O. , Sastry Anand V. 
Published: December 2021

AbstractBackgroundIndependent component analysis is an unsupervised machine learning algorithm that separates a set of mixed signals into a set of statistically independent source signals. Applied to high-quality gene expression datasets, independent component analysis effectively reveals both the source signals of the transcriptome as co-regulated gene sets, and the activity levels of the underlying regulators across diverse experimental conditions. Two major variables that affect the final gene sets are the diversity of the expression profiles contained in the underlying data, and the user-defined number of independent components, or dimensionality, to compute. Availability of high-quality transcriptomic datasets has grown exponentially as high-throughput technologies have advanced; however, optimal dimensionality selection remains an open question.MethodsWe computed independent components across a range of dimensionalities for four gene expression datasets with varying dimensions (both in terms of number of genes and number of samples). We computed the correlation between independent components across different dimensionalities to understand how the overall structure evolves as the number of user-defined components increases. We then measured how well the resulting gene clusters reflected known regulatory mechanisms, and developed a set of metrics to assess the accuracy of the decomposition at a given dimension.ResultsWe found that over-decomposition results in many independent components dominated by a single gene, whereas under-decomposition results in independent components that poorly capture the known regulatory structure. From these results, we developed a new method, called OptICA, for finding the optimal dimensionality that controls for both over- and under-decomposition. Specifically, OptICA selects the highest dimension that produces a low number of components that are dominated by a single gene. We show that OptICA outperforms two previously proposed methods for selecting the number of independent components across four transcriptomic databases of varying sizes.ConclusionsOptICA avoids both over-decomposition and under-decomposition of transcriptomic datasets resulting in the best representation of the organism’s underlying transcriptional regulatory network.
The cold - resistance mechanism of a mutagenic Volvariella volvacea strain VH3 with outstanding traits revealed by transcriptome profiling
Authors: Li Peng , Hu Cong , Li Yujie , Ge Lei , Wu Guogan , Lv Beibei , Jiang Wei , Xi Dandan 
Published: December 2021

Abstract
Background
The straw mushroom (Volvariella volvacea) is one of the important vegetables that is popular for its delicious taste. However, the straw mushroom is sensitive to low temperature, resulting in economic loss during transportation and storage. We obtained a novel straw mushroom strain, named VH3, via ultraviolet mutagenesis.

Results
Our study revealed that VH3 exhibited high cold resistance compared to an ordinary straw mushroom cultivar, V23. We found that the electrolyte leakages of VH3 were always significantly lower than that of V23 treated with 4 °C for 0 h, 2 h,4 h, 8 h, 16 h, and 24 h. Before cold treatment (0 h), there were no difference of MDA contents, SOD activities, and CAT activities between VH3 and V23. At the late stage (8 h, 26 h, and 24 h) of cold treatment, the MDA contents of VH3 were lower while both the SOD and CAT activities were higher than those of V23. To investigate the potential mechanisms of VH3 cold resistance, we performed transcriptome sequencing to detect the transcriptome profiling of VH3 and V23 after 0 h and 4 h cold treatment. Transcriptome sequencing revealed that 111 differentially expressed genes (DEG) between V23 (0 h) and VH3 (0 h) (V23–0_vs_VH3–0), consisting 50 up-regulated and 61 down-regulated DEGs. A total of 117 DEGs were obtained between V23 (4 h) and VH3(4 h) (V23–4_vs_VH3–4), containing 94 up-regulated and 23 down-regulated DEGs. Among these DEGs, VVO_00021 and VVO_00017 were up-regulated while VVO_00003, VVO_00004, VVO_00010, and VVO_00030 were down-regulated in V23–0_vs_VH3–0 and VH3–4_vs_V23–4. KEGG and GO analysis revealed that the 6 DEGs were annotated to pathways related to cold stress. Besides, the GA3 content was also decreased in VH3.

Conclusions
Collectively, our study first revealed that the increased cold resistance of VH3 might be caused by the expression change of VVO_00003, VVO_00004, VVO_00017, VVO_00021, and VVO_00030, and decreased GA3.
Identifying comorbidities and lifestyle factors contributing to the cognitive profile of early Parkinson’s disease
Authors: Martínez-Horta Saul , Bejr-Kasem Helena , Horta-Barba Andrea , Pascual-Sedano Berta , Santos-García Diego , de Deus-Fonticoba Teresa , Jesús Silvia , Aguilar Miquel , Planellas Lluis , García-Caldentey Juan , Caballol Nuria , Vives-Pastor Bárbara , Hernández-Vara Jorge , Cabo-Lopez Iria , López-Manzanares Lydia , González-Aramburu Isabel , Ávila-Rivera Maria Asunción , Catalán Maria Jose , López-Díaz Luis Manuel , Puente Victor , García-Moreno Jose Manuel , Borrué Carmen , Solano-Vila Berta , Álvarez-Sauco Maria , Vela Lydia , Escalante Sonia , Cubo Esther , Carrillo-Padilla Francisco , Martínez-Castrillo Juan Carlos , Sánchez-Alonso Pilar , Alonso-Losada Maria Gema , López-Ariztegui Nuria , Gastón Itziar , Blázquez-Estrada Marta , Seijo-Martínez Manual , Rúiz-Martínez Javier , Valero-Merino Caridad , Kurtis Monica , de Fábregues-Boixar Oriol , González-Ardura Jessica , Prieto-Jurczynska Cristina , Martinez-Martin Pablo , Mir Pablo , Kulisevsky Jaime ,   COPPADIS Study Group
Published: December 2021

Abstract
Background
Identifying modifiable risk factors for cognitive impairment in the early stages of Parkinson’s disease (PD) and estimating their impact on cognitive status may help prevent dementia (PDD) and the design of cognitive trials.

Methods
Using a standard approach for the assessment of global cognition in PD and controlling for the effects of age, education and disease duration, we explored the associations between cognitive status, comorbidities, metabolic variables and lifestyle variables in 533 PD participants from the COPPADIS study.

Results
Among the overall sample, 21% of participants were classified as PD-MCI (n = 114) and 4% as PDD (n = 26). The prevalence of hypertension, diabetes and dyslipidemia was significantly higher in cognitively impaired patients while no between-group differences were found for smoking, alcohol intake or use of supplementary vitamins. Better cognitive scores were significantly associated with regular physical exercise (p < 0.05) and cognitive stimulation (< 0.01). Cognitive performance was negatively associated with interleukin 2 (Il2) (p < 0.05), Il6 (p < 0.05), iron (p < 0.05), and homocysteine (p < 0.005) levels, and positively associated with vitamin B12 levels (p < 0.005).

Conclusions
We extend previous findings regarding the positive and negative influence of various comorbidities and lifestyle factors on cognitive status in early PD patients, and reinforce the need to identify and treat potentially modifiable variables with the intention of exploring the possible improvement of the global cognitive status of patients with PD.
Communicating with patients and families about illness progression and end of life: a review of studies using direct observation of clinical practice
Authors: Ekberg Stuart , Parry Ruth , Land Victoria , Ekberg Katie , Pino Marco , Antaki Charles , Jenkins Laura , Whittaker Becky 
Published: December 2021

Abstract
Background
There is growing recognition that a diverse range of healthcare professionals need competence in palliative approaches to care. Effective communication is a core component of such practice. This article informs evidence-based communication about illness progression and end of life through a rapid review of studies that directly observe how experienced clinicians manage such discussions.

Methods
The current rapid review updates findings of a 2014 systematic review, focussing more specifically on evidence related to illness progression and end-of-life conversations. Literature searches were conducted in nine bibliographic databases. Studies using conversation analysis or discourse analysis to examine recordings of actual conversations about illness progression or end of life were eligible for inclusion in the review. An aggregative approach was used to synthesise the findings of included studies.

Results
Following screening, 26 sources were deemed to meet eligibility criteria. Synthesis of study findings identified the structure and functioning of ten communication practices used in discussions about illness progression and end-of-life.

Conclusion
The ten practices identified underpin five evidence-based recommendations for communicating with patients or family members about illness progression and end of life.
How can we improve the experiences of patients and families who request medical assistance in dying? A multi-centre qualitative study
Authors: Oczkowski Simon J. W. , Crawshaw Diane E. , Austin Peggy , Versluis Donald , Kalles-Chan Gaelen , Kekewich Michael , Curran Dorothyann , Miller Paul , Kelly Michaela , Wiebe Ellen , Frolic Andrea 
Published: December 2021

Abstract
Background
Medical assistance in dying has been available in Canada for 5 years, but it is unclear which practices contribute to high-quality care. We aimed to describe patient and family perspectives of quality of care for medical assistance in dying.

Methods
We conducted a multi-centre, qualitative descriptive study, including face to face or virtual one-hour interviews using a semi-structured guide. We interviewed 21 english-speaking patients found eligible for medical assistance in dying and 17 family members at four sites in Canada, between November 2017 and September 2019. Interviews were de-identified, and analyzed in an iterative process of thematic analysis.

Results
We identified 18 themes. Sixteen themes were related to a single step in the process of medical assistance in dying (MAID requests, MAID assessments, preparation for dying, death and aftercare). Two themes (coordination and patient-centred care) were theme consistently across multiple steps in the MAID process. From these themes, alongside participant recommendations, we developed clinical practice suggestions which can guide care.

Conclusions
Patients and families identified process-specific successes and challenges during the process of medical assistance in dying. Most importantly, they identified the need for care coordination and a patient-centred approach as central to high-quality care. More research is required to characterize which aspects of care most influence patient and family satisfaction.
Anemia can predict the prognosis of colorectal cancer in the pre-operative stage: a retrospective analysis
Authors: Gvirtzman Rotem , Livovsky Dan Meir , Tahover Esther , Goldin Eran , Koslowsky Benjamin 
Published: December 2021

Abstract
Background
Early detection of colorectal cancer (CRC) improves prognosis, yet many CRCs are diagnosed following symptoms. The aim of this study was to determine which CRC-related symptoms or signs can predict an advanced CRC in the pre-operative stage.

Methods
Retrospective analysis of 300 patients who underwent surgery for CRC between the years 2008 and 2019. Patients’ symptoms prior to CRC diagnosis were documented. Primary endpoint was the association of signs or/and symptoms with CRC diagnosis at TNM stages of 2–4 (i.e., highly advanced), compared to TNM score of 0–1 (i.e., locally advanced).

Results
Three hundred patients, 91 with locally advanced and 209 with highly advanced CRC, were enrolled. There was a significant correlation between highly advanced CRC, compared to locally advanced, regarding tumor size (4.8 vs. 2.6 cm, p<0.001), presentation of any symptom prior to diagnosis (77% vs. 54%, p<0.001), anemia (46% vs. 29%, p=0.004), and severe anemia (17% vs. 4%, p=0.002). Mean hemoglobin was 12.2 ± 2.2 and 13.1 ± 1.8 in the highly advanced compared to locally advanced CRC, respectively, p<0.001. Anemia correlated with the T stage of the tumor: 21% of patients diagnosed at stages 0–1 had anemia, 39% at stage 2, 44% at stage 3, and 66% at stage 4 (p=0.001).

Conclusions
Anemia is the only finding that correlates with highly advanced CRC, in the pre-operative stage. When CRC has been diagnosed, the presence of anemia, at any level, may be considered in determining prognosis at the pre-operative stage. Physicians should be aware that when anemia is present, the risk for highly advanced CRC increases, and therefore should pursue with CRC detection.
Development of a radiographic scoring system for new bone formation in gout
Authors: Son Chang-Nam , Cai Ken , Stewart Sarah , Ferrier John , Billington Karen , Tsai Yun-Jung Jack , Bardin Thomas , Horne Anne , Stamp Lisa K. , Doyle Anthony , Dalbeth Nicola 
Published: December 2021

Abstract
Background
Features of new bone formation (NBF) are common in tophaceous gout. The aim of this project was to develop a plain radiographic scoring system for NBF in gout.

Methods
Informed by a literature review, scoring systems were tested in 80 individual 1st and 5th metatarsophalangeal joints. Plain radiography scores were compared with computed tomography (CT) measurements of the same joints. The best-performing scoring system was then tested in paired sets of hand and foot radiographs obtained over 2 years from an additional 25 patients. Inter-reader reproducibility was assessed using intraclass correlation coefficients (ICC). NBF scores were correlated with plain radiographic erosion scores (using the gout-modified Sharp-van der Heijde system).

Results
Following a series of structured reviews of plain radiographs and scoring exercises, a semi-quantitative scoring system for sclerosis and spur was developed. In the individual joint analysis, the inter-observer ICC (95% CI) was 0.84 (0.76–0.89) for sclerosis and 0.81 (0.72–0.87) for spur. Plain radiographic sclerosis and spur scores correlated with CT measurements (r = 0.65–0.74, P < 0.001 for all analyses). For the hand and foot radiograph sets, the inter-observer ICC (95% CI) was 0.94 (0.90–0.98) for sclerosis score and 0.76 (0.65–0.84) for spur score. Sclerosis and spur scores correlated highly with plain radiographic erosion scores (r = 0.87 and 0.71 respectively), but not with change in erosion scores over 2 years (r = −0.04–0.15).

Conclusion
A semi-quantitative plain radiographic scoring method for the assessment of NBF in gout is feasible, valid, and reproducible. This method may facilitate consistent measurement of NBF in gout.
Evolution of anti-modified protein antibody responses can be driven by consecutive exposure to different post-translational modifications
Authors: Volkov M. , Kampstra A. S. B. , van Schie K. A. , Kawakami A. , Tamai M. , Kawashiri S. , Maeda T. , Huizinga T. W. J. , Toes R. E. M. , van der Woude D. 
Published: December 2021

Abstract
Background
Besides anti-citrullinated protein antibodies (ACPA), rheumatoid arthritis patients (RA) often display autoantibody reactivities against other post-translationally modified (PTM) proteins, more specifically carbamylated and acetylated proteins. Immunizing mice with one particular PTM results in an anti-modified protein antibody (AMPA) response recognizing different PTM-antigens. Furthermore, human AMPA, isolated based on their reactivity to one PTM, cross-react with other PTMs. However, it is unclear whether the AMPA-reactivity profile is “fixed” in time or whether consecutive exposure to different PTMs can shape the evolving AMPA response towards a particular PTM.

Methods
Longitudinally collected serum samples of 8 human individuals at risk of RA and 5 with early RA were tested with ELISA, and titers were analyzed to investigate the evolution of the AMPA responses over time. Mice (13 per immunization group in total) were immunized with acetylated (or carbamylated) protein (ovalbumin) twice or cross-immunized with an acetylated and then a carbamylated protein (or vice versa) and their serum was analyzed for AMPA responses.

Results
Human data illustrated dynamic changes in AMPA-reactivity profiles in both individuals at risk of RA and in early RA patients. Mice immunized with either solely acetylated or carbamylated ovalbumin (AcOVA or CaOVA) developed reactivity against both acetylated and carbamylated antigens. Irrespective of the PTM-antigen used for the first immunization, a booster immunization with an antigen bearing the other PTM resulted in increased titers to the second/booster PTM. Furthermore, cross-immunization skewed the overall AMPA-response profile towards a relatively higher reactivity against the “booster” PTM.

Conclusions
The relationship between different reactivities within the AMPA response is dynamic. The initial exposure to a PTM-antigen induces cross-reactive responses that can be boosted by an antigen bearing this or other PTMs, indicating the formation of cross-reactive immunological memory. Upon subsequent exposure to an antigen bearing another type of PTM, the overall reactivity pattern can be skewed towards better recognition of the later encountered PTM. These data might explain temporal differences in the AMPA-response profile and point to the possibility that the PTM responsible for the initiation of the AMPA response may differ from the PTM predominantly recognized later in time.
Water resilience mapping of Chennai, India using analytical hierarchy process
Authors: Kaaviya R. , Devadas V. 
Published: December 2021

Abstract
Background
The urban water system is the worst hit in global climate change. Water resilience is the system’s ability to retaliate and recover from various water-related disruptions. The present study aims to delineate the water resilience zones in Chennai city, Tamil Nadu, India, by effectively integrating the geographic information system, remote sensing, and analytical hierarchy process (AHP).

Methods
The methodology incorporated 15 vital factors. A multi-criteria decision analysis technique was adopted to assign a weight to each parameter using the AHP. A pairwise decision matrix was constructed, parameter’s relative importance and the consistency ratio were established. Integration of all maps by weighted overlay analysis technique depicted water resilience intensities of five different classes.

Results
Very low, low and moderate water resilience areas accounted for more than three-fourth of the study area. Area Under Curve score (80.12%) depicted the accuracy of the developed model. Sensitivity analysis determined the significance of the parameters in the delineation. The logical structural approach can be employed in other parts of India or elsewhere with modifications.

Conclusion
This study is novel in its approach by holistically analyzing water resilience by integrating disruptions related to flood, drought and the city's water infrastructure system's adequacy and efficiency. Researchers and planners can effectively use the study results to ensure resilience as a new perspective on effective water resource management and climate change mitigation. It becomes a decision aid mechanism identifying where the system is vulnerable to potential water-related risks for employing resilience measures.
Optimal sites for orthodontic anchor screw placement using panoramic images: risk of maxillary sinus perforation and contact with adjacent tooth roots during screw placement
Authors: Miyazawa Ken , Shibata Momoko , Tabuchi Masako , Kawaguchi Misuzu , Shimura Noriko , Goto Shigemi 
Published: December 2021

AbstractObjectivesThis study investigated the safety of orthodontic anchor screw (OAS) placement by examining the morphology and degree of depression of the maxillary sinus adjacent to the alveolar bone between the maxillary molars.MethodsWe reviewed panoramic and CT imaging data of 25 patients. First, the morphology of the maxillary sinus adjacent to the alveolar bone between the maxillary molars on panoramic images was classified into three types: non-depressed sinus, funnel-like sinus depression, and sawtooth-like sinus depression. Then, the distance from the maxillary buccal bone to the maxillary sinus or to the maxillary lingual bone and the distance between the roots of the maxillary second premolar and first molar at heights of 5, 6.5, and 8 mm from the alveolar crest were measured on CT images and compared between the three sinus morphology groups.ResultsThe sawtooth-like depression group had significantly smaller bone thickness than the other two groups, with mean thickness of < 4 mm at any height from the alveolar crest. The funnel-like depression and non-depression groups had mean bone thickness of > 8 mm at any height from the alveolar crest.ConclusionsSawtooth-like sinus depression had increased risk of maxillary sinus perforation, suggesting that OAS placement in this region should be avoided. In contrast, OAS placement between 6.5 and 8 mm from the alveolar crest is advisable in patients with funnel-like sinus depression and at a site > 8 mm from the alveolar crest in those with a non-depressed sinus.