bluuebunny/crossref_metadata_2025_split huggingface dataset:
Paper 18: Treatment of Lateral Meniscus Tears Influences OA Rate following ACL Reconstruction at 9-year Follow-Up
Authors: Briggs Karen , Petterson Stephanie , Plancher Kevin 
Published: May 2022

Objectives: Recent studies have described an increased risk of osteoarthritis (OA) following ACL reconstruction (ACLR). Systematic reviews have suggested that meniscal pathology, which occurs in up to 60% of patients with ACL injury, increases this risk. The purpose of this study was to determine the influence of lateral meniscus tears and repair versus partial lateral meniscectomy on the risk of OA in patients following ACLR. Methods: All patients who underwent primary autograft or allograft bone-patellar tendon-bone (BPTB) transtibial ACLR by a single surgeon between 1999-2019, were identified. Revision ACLR, multi-ligamentous reconstructions, and patients with less than 2-year imaging follow-up were excluded. Patients with lateral meniscus pathology at the time of ACLR were identified and treatment (e.g. lateral meniscectomy or lateral meniscus tear) was extracted. OA was defined at follow-up as Kellgren-Lawrence (KL) grade III-IV on plain radiographs. Chi-square tests assessed differences in incidence rates (p<0.05). Results: A consecutive series of 113 patients (57 males, 56 females; age 35.7±11.9 years) with BPTB ACLR were included. The mean follow-up was 9±5 years. The prevalence of lateral meniscus tears was 60.2% (68/113) and the prevalence of lateral compartment OA at follow-up was 14% (16/113) Patients with a lateral meniscus tear were 4.7 times more likely to develop OA compared to patients with no lateral meniscus tear. 20.6% of patients (14/68) with lateral meniscus tear developed lateral OA compared to 4.4% of patients (2/45) without lateral meniscus tear (p=0.0158). Patients who underwent lateral meniscal repair (n=16) had significantly lower prevalence of OA (0/16) compared to patients who underwent lateral meniscectomy (14/52) (p=0.0196). Conclusions: At nine-year follow-up, patients with a lateral meniscus tear at time of ACLR were more likely to develop OA compared to patients with no lateral meniscus tear and patients treated with partial meniscectomy had higher prevalence of OA compared to those treated with meniscus repair. In patients who require ACLR, care should be taken in evaluating and treating the lateral meniscus to decrease the likelihood of the development of OA. We believe lateral meniscal repair is essential for lateral meniscus tears at the time ACL reconstruction to help avoid development of OA. [Figure: see text]
Paper 23: Long Term Outcomes After Arthroscopic Treatment of Femoroacetabular Impingement for Patients with Borderline Dysplasia
Authors: Day Molly , Olsen Reena , Buza Stephanie , Kelly Bryan , Ranawat Anil , Nawabi Danyal , Selley Ryan 
Published: May 2022

Objectives: Outcomes following isolated hip arthroscopy for patients with dysplasia have been unfavorable, results have included iatrogenic instability and conversion to total hip arthroplasty (THA) at a young age. However, patients with borderline dysplasia have portended more favorable results at short and medium term follow-up. The purpose of this study was to assess long term outcomes after hip arthroscopy for femoroacetabular impingement (FAI) in borderline dysplasia (BD) patients (LCEA, 18°-25°) compared to a control cohort of nondysplastic patients (LCEA, 25°-40°). Methods: Between March 2009 and July 2012, a BD group of 33 patients (38 hips) was identified. An age- and sex-matched control group of 83 patients (96 hips) was also identified. Patient-reported outcome scores, including the modified Harris Hip Score (mHHS), the Hip Outcome Score–Activities of Daily Living (HOS-ADL) and Sport-Specific Subscale (HOS-SSS), and the International Hip Outcome Tool (iHOT-33), were collected preoperatively and subsequently at an average of 9.6 years post-operatively. Results: The mean LCEA and Tönnis angle was 22.4° ± 2.02° and 6.2° ± 3.23° in the BD group and 31.7° ± 3.52° and 2.42° ± 3.02° in the control group, respectively ( P <0.001). A labral repair was performed in 78.9% and 76% of the BD and control groups, respectively, all patients underwent capsular closure as part of routine hip arthroscopy. A cam decompression was performed in 97.4% of the BD patients and 99.0% of the control patients. At mean follow-up of 9.6 years (range, 8.2-11.6 years) on average there was significant improvement in all patient-reported outcomes scores in both groups (P<0.001). There were no significant differences between pre and post-operative scores between BD and control groups. Two hips (5.2%) underwent revision surgery in the BD group and 10 hips (10.4%) in the control group, of these one patient in the BD group underwent THA and one patient who underwent bilateral hip arthroscopies in the control group underwent bilateral hip resurfacing. Conclusions: Durable outcomes (>9 years) with low revision rates can be expected after isolated hip arthroscopy that includes cam resection, labral refixation and capsular closure in BD patients with equivalent outcomes to a nondysplastic cohort.
Paper 26: Defining Clinically Significant Improvement on Patient-Reported Outcomes Measurement Information System Test for Patients Undergoing Hip Arthroscopy for the Treatment of Femoroacetabular Impingement Syndrome at 1-Year Follow-Up
Authors: Clapp Ian , DeFroda Steven , Newhouse Alexander , Alter Thomas , Nwachukwu Ben , Nho Shane , Bodendorfer Blake 
Published: May 2022

Objectives: While minimal clinically important difference (MCID), patient acceptable symptomatic state (PASS), and substantial clinical benefit (SCB) have been defined for hip-specific legacy patient reported outcome measures, they have not been defined for the Patient-Reported Outcomes Measurement Information System (PROMIS) instruments for patients undergoing hip arthroscopy. The purpose of the study was to define the MCID, PASS, and SCB thresholds for the PROMIS Physical Function (PF) computerized adaptive test (CAT) and PROMIS Pain Interference (PI) instruments in patients undergoing hip arthroscopy for femoroacetabular impingement syndrome (FAIS). Methods: Patients undergoing primary hip arthroscopy between August 2018 and January 2019 for the treatment of FAIS were retrospectively analyzed. Patients received PROMIS-PF, PROMIS-PI, Hip Outcome Score Activities of Daily Living, Hip Outcome Score Sport Subscale, modified Harris Hip Score, and international Hip Outcome Tool-12 preoperatively and at 1 year postoperatively. MCID was calculated using the distribution method, while PASS and SCB were calculated using an anchor-based method. Patients achieving clinically significant outcomes (CSOs) were compared to those who failed to achieve via chi-square and independent sample t-tests, and a multivariate logistic regression was conducted to determine predictors of CSO achievement. Results: 124 patients with an average age of 32.7±12.3 were included in the analysis. The threshold scores required to achieve MCID, PASS, and SCB, respectively, were as follows: PROMIS-PI (-3.1, 53.7, 51.9) and PROMIS-PF (3.3, 47.0, 49.9). Patients achieved any MCID, PASS, and SCB for PROMIS scores at a rate of 89.0%, 71.8%, and 62.1%, respectively compared to 87.1%, 76.6%, and 71.8% for legacy PROMs. For PROMIS-PF, higher preoperative PROMIS-PF score was a positive predictor of CSO achievement, and patients achieving SCB were significantly younger (30.3±12 vs 35.6±12, p=0.017) with significantly lower BMIs (24.7±6.4 vs. 27.9±7, p=0.009). Preoperative chronic pain and past history of orthopaedic surgery were negative predictors of PROMIS-PI CSO achievement while higher (worse) preoperative PROMIS-PI scores were a positive predictor. Conclusions: Our study defined the MCID, PASS, and SCB for the PROMIS PF and PI CAT at 1-year postoperatively. CSO is achieved via PROMIS at a rate comparable, but slightly less than legacy hip PROMs. In addition, patients with higher preoperative PROMIS scores, younger age, and lower BMIs were more likely to achieve a CSO while preoperative chronic pain and past history of orthopaedic surgery were negative predictors of CSO achievement.
Research on preparation technology of animal skin intrinsic multifunctional packaging material
Authors: Zhang Jiaxing , Long Zhongzhen , Chen Hui , Shan Zhihua 
Published: May 2022

High-end leather packaging material safe, environmentally friendly, and has a good market prospect. It is an interesting technology to solve the intrinsic functionalization of skin collagen packaging materials. Nano-Hydroxyapatite (HA) precursors solution with a specific 1.67 calcium to phosphorus ratio (Ca/P) were infiltrated into the three-dimensional collagen network matrix (3DCM) in situ growth based on goat skin pretreated with glutaraldehyde and the HAG-3DCM was obtained. After compression, a transparent film HAG-3DCM-was formed. Structural and functional characterization showed that the HAG-3DCM-CM film has good comprehensive performance, such as the tensile strength increased to 67 mPa from 28 mPa, the bending resistance increased from 5 cycles to 50 cycles and the swelling degree from 55% to 12%. HA disperses and fixes the three-dimensional collagen network matrix (3DCM) fibers, improves its stability against humidity and heat, and the thermal conductivity changed from 0.72 W/(K•m) to 0.65 W/(K•m). HAG-3DCM has a relatively high limiting oxygen index of 26.5%. This study demonstrates a new approach for preparing animal skin packaging materials with new application value.
Proteomic alteration of endometrial tissues during secretion in polycystic ovary syndrome may affect endometrial receptivity
Authors: Li Jun , Jiang Xiaohua , Li Caihua , Che Huihui , Ling Lin , Wei Zhaolian 
Published: May 2022

AbstractEmbryo implantation is a complex developmental process that requires coordinated interactions among the embryo, endometrium, and the microenvironment of endometrium factors. Even though the impaired endometrial receptivity of patients with polycystic ovary syndrome (PCOS) is known, understanding of endometrial receptivity is limited. A proteomics study in three patients with PCOS and 3 fertile women was performed to understand the impaired endometrial receptivity in patients with PCOS during luteal phases. Through isobaric tags for relative and absolute quantitation (iTRAQ) analyses, we identified 232 unique proteins involved in the metabolism, inflammation, and cell adhesion molecules. Finally, our results suggested that energy metabolism can affect embryo implantation, whereas inflammation and cell adhesion molecules can affect both endometrial conversion and receptivity. Our results showed that endometrial receptive damage in patients with PCOS is not a single factor. It is caused by many proteins, pathways, systems, and abnormalities, which interact with each other and make endometrial receptive research more difficult.
Thermal gradient ring reveals different temperature-dependent behaviors in mice lacking thermosensitive TRP channels
Authors: Ujisawa Tomoyo , Sasajima Sachiko , Kashio Makiko , Tominaga Makoto 
Published: May 2022

AbstractTransient receptor potential (TRP) channels are known as temperature receptors. Each channel has an activation temperature in vitro within the physiological temperature range. Mice deficient in specific TRP channels show abnormal thermal behaviors. However, the role of TRP channels in mouse thermal behavior is not fully understood. We measured thermal behavior using a new type of thermal gradient system, where mice can freely move around the ring floor, thereby avoiding the stereotypical habit that mice have of staying in a corner, as occurs in a rectangular system. With this system, we can also analyze various factors, such as “Spent time,” “Travel distance,” “Moving speed,” and “Acceleration,” to provide more accurate information about mouse behaviors. Further analysis using this system would lead to a better understanding of the molecular basis of thermal behaviors in mice, which could help us develop ways of making humans comfortable in different temperature conditions.
FragGeneScanRs: faster gene prediction for short reads
Authors: Van der Jeugt Felix , Dawyndt Peter , Mesuere Bart 
Published: May 2022

Abstract
Background
FragGeneScan is currently the most accurate and popular tool for gene prediction in short and error-prone reads, but its execution speed is insufficient for use on larger data sets. The parallelization which should have addressed this is inefficient. Its alternative implementation FragGeneScan+ is faster, but introduced a number of bugs related to memory management, race conditions and even output accuracy.

Results
This paper introduces FragGeneScanRs, a faster Rust implementation of the FragGeneScan gene prediction model. Its command line interface is backward compatible and adds extra features for more flexible usage. Its output is equivalent to the original FragGeneScan implementation.

Conclusions
Compared to the current C implementation, shotgun metagenomic reads are processed up to 22 times faster using a single thread, with better scaling for multithreaded execution. The Rust code of FragGeneScanRs is freely available from GitHub under the GPL-3.0 license with instructions for installation, usage and other documentation (https://github.com/unipept/FragGeneScanRs).
Toward a more accurate 3D atlas of C. elegans neurons
Authors: Skuhersky Michael , Wu Tailin , Yemini Eviatar , Nejatbakhsh Amin , Boyden Edward , Tegmark Max 
Published: May 2022

Abstract
Background
Determining cell identity in volumetric images of tagged neuronal nuclei is an ongoing challenge in contemporary neuroscience. Frequently, cell identity is determined by aligning and matching tags to an “atlas” of labeled neuronal positions and other identifying characteristics. Previous analyses of such C. elegans datasets have been hampered by the limited accuracy of such atlases, especially for neurons present in the ventral nerve cord, and also by time-consuming manual elements of the alignment process.

Results
We present a novel automated alignment method for sparse and incomplete point clouds of the sort resulting from typical C. elegans fluorescence microscopy datasets. This method involves a tunable learning parameter and a kernel that enforces biologically realistic deformation. We also present a pipeline for creating alignment atlases from datasets of the recently developed NeuroPAL transgene. In combination, these advances allow us to label neurons in volumetric images with confidence much higher than previous methods.

Conclusions
We release, to the best of our knowledge, the most complete full-body C. elegans 3D positional neuron atlas, incorporating positional variability derived from at least 7 animals per neuron, for the purposes of cell-type identity prediction for myriad applications (e.g., imaging neuronal activity, gene expression, and cell-fate).
miR-155 exerts posttranscriptional control of autoimmune regulator (Aire) and tissue-restricted antigen genes in medullary thymic epithelial cells
Authors: Tanaka Pedro Paranhos , Oliveira Ernna Hérida , Vieira-Machado Mayara Cristina , Duarte Max Jordan , Assis Amanda Freire , Bombonato-Prado Karina Fittipaldi , Passos Geraldo Aleixo 
Published: May 2022

Abstract
Background
The autoimmune regulator (Aire) gene is critical for the appropriate establishment of central immune tolerance. As one of the main controllers of promiscuous gene expression in the thymus, Aire promotes the expression of thousands of downstream tissue-restricted antigen (TRA) genes, cell adhesion genes and transcription factor genes in medullary thymic epithelial cells (mTECs). Despite the increasing knowledge about the role of Aire as an upstream transcriptional controller, little is known about the mechanisms by which this gene could be regulated.

Results
Here, we assessed the posttranscriptional control of Aire by miRNAs. The in silico miRNA-mRNA interaction analysis predicted thermodynamically stable hybridization between the 3’UTR of Aire mRNA and miR-155, which was confirmed to occur within the cellular milieu through a luciferase reporter assay. This finding enabled us to hypothesize that miR-155 might play a role as an intracellular posttranscriptional regulator of Aire mRNA. To test this hypothesis, we transfected a murine mTEC cell line with a miR-155 mimic in vitro, which reduced the mRNA and protein levels of Aire. Moreover, large-scale transcriptome analysis showed the modulation of 311 downstream mRNAs, which included 58 TRA mRNAs. Moreover, miR-155 mimic-transfected cells exhibited a decrease in their chemotaxis property compared with control thymocytes.

Conclusion
Overall, the results indicate that miR-155 may posttranscriptionally control Aire mRNA, reducing the respective Aire protein levels; consequently, the levels of mRNAs encode tissue-restricted antigens were affected. In addition, miR-155 regulated a crucial process by which mTECs allow thymocytes’ migration through chemotaxis.
A comparison of methods for multiple degree of freedom testing in repeated measures RNA-sequencing experiments
Authors: Wynn Elizabeth A. , Vestal Brian E. , Fingerlin Tasha E. , Moore Camille M. 
Published: May 2022

AbstractBackgroundAs the cost of RNA-sequencing decreases, complex study designs, including paired, longitudinal, and other correlated designs, become increasingly feasible. These studies often include multiple hypotheses and thus multiple degree of freedom tests, or tests that evaluate multiple hypotheses jointly, are often useful for filtering the gene list to a set of interesting features for further exploration while controlling the false discovery rate. Though there are several methods which have been proposed for analyzing correlated RNA-sequencing data, there has been little research evaluating and comparing the performance of multiple degree of freedom tests across methods.MethodsWe evaluated 11 different methods for modelling correlated RNA-sequencing data by performing a simulation study to compare the false discovery rate, power, and model convergence rate across several hypothesis tests and sample size scenarios. We also applied each method to a real longitudinal RNA-sequencing dataset.ResultsLinear mixed modelling using transformed data had the best false discovery rate control while maintaining relatively high power. However, this method had high model non-convergence, particularly at small sample sizes. No method had high power at the lowest sample size. We found a mix of conservative and anti-conservative behavior across the other methods, which was influenced by the sample size and the hypothesis being evaluated. The patterns observed in the simulation study were largely replicated in the analysis of a longitudinal study including data from intensive care unit patients experiencing cardiogenic or septic shock.ConclusionsMultiple degree of freedom testing is a valuable tool in longitudinal and other correlated RNA-sequencing experiments. Of the methods that we investigated, linear mixed modelling had the best overall combination of power and false discovery rate control. Other methods may also be appropriate in some scenarios.
An approach to exploring patterns of imbalance and potential missingness in reports of the randomized baseline values for primary outcomes measurable at baseline in randomized controlled trials for meta-analyses
Authors: Park Eun-Gee , Hahn Seokyung 
Published: May 2022

Abstract
Background
This study evaluated the adequacy of randomization in randomized controlled trials by investigating baseline differences in the primary outcome when a meta-analysis employed an outcome whose baseline level was measurable.

Methods
We retrieved Cochrane reviews published during one year. We calculated the proportion of studies that reported randomized baseline values for the primary outcome. The standardized mean difference (SMD) was used to assess baseline imbalance and heterogeneity. We explored ranking-ordered forest plots using a normal cumulative probability curve as a guideline representing well-performed randomized trials. When skewness was suggested, a funnel plot was drawn to assess whether there was a significant linear trend.

Results
In 10 of 18 meta-analyses, more than 25% of trials did not report randomized baseline values of the primary outcomes. Three meta-analyses indicated baseline imbalance (P < 0.1) and three showed substantial heterogeneity (I2 > 60%). Four meta-analyses with forest plots suggesting a skewed SMD distribution also showed a linear trend on their standard errors on the funnel plot.

Conclusions
If the primary outcome is measured at baseline, it is essential to explore the full scope of baseline imbalance among the trials. This could help understand patterns of bias, including missingness, for designing adjustment.
Using observational study data as an external control group for a clinical trial: an empirical comparison of methods to account for longitudinal missing data
Authors: Norvang Vibeke , Haavardsholm Espen A. , Tedeschi Sara K. , Lyu Houchen , Sexton Joseph , Mjaavatten Maria D. , Kvien Tore K. , Solomon Daniel H. , Yoshida Kazuki 
Published: May 2022

Abstract
Background
Observational data are increasingly being used to conduct external comparisons to clinical trials. In this study, we empirically examined whether different methodological approaches to longitudinal missing data affected study conclusions in this setting.

Methods
We used data from one clinical trial and one prospective observational study, both Norwegian multicenter studies including patients with recently diagnosed rheumatoid arthritis and implementing similar treatment strategies, but with different stringency. A binary disease remission status was defined at 6, 12, and 24 months in both studies. After identifying patterns of longitudinal missing outcome data, we evaluated the following five approaches to handle missingness: analyses of patients with complete follow-up data, multiple imputation (MI), inverse probability of censoring weighting (IPCW), and two combinations of MI and IPCW.

Results
We found a complex non-monotone missing data pattern in the observational study (N = 328), while missing data in the trial (N = 188) was monotone due to drop-out. In the observational study, only 39.0% of patients had complete outcome data, compared to 89.9% in the trial. All approaches to missing data indicated favorable outcomes of the treatment strategy in the trial and resulted in similar study conclusions. Variations in results across approaches were mainly due to variations in estimated outcomes for the observational data.

Conclusions
Five different approaches to handle longitudinal missing data resulted in similar conclusions in our example. However, the extent and complexity of missing observational data affected estimated comparative outcomes across approaches, highlighting the need for careful consideration of methods to account for missingness in this setting. Based on this empirical examination, we recommend using a prespecified advanced missing data approach to account for longitudinal missing data, and to conduct alternative approaches in sensitivity analyses.