bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biomechanical characteristics of transfemoral bone-anchored prostheses during gait: A review of literature
Authors: Ravari Reihaneh , Rehani Mayank , Hebert Jacqueline S. 
Published: August 2023

Background:
Osseointegration (OI) is an emerging technique that allows a direct connection between the bone and a titanium metal implant, allowing the direct attachment of bone-anchored prostheses (BAP) to address the problems associated with socket prostheses. This review article aims to compare the biomechanical features of gait when using a transfemoral BAP in comparison to healthy gait, and in comparison to the gait of traditional transfemoral socket prosthesis users.

Methods:
A computer-based literature search of electronic databases since inception (ranging from 1967 to 2004 depending on the database) to June 14, 2022, identified peer-reviewed articles focusing on the temporal-spatial, kinematic, kinetic, and electromyography data related to transfemoral BAP gait. Eight articles were included that focused on these biomechanical features of gait in adults with BAP and were compared with socket prosthesis users or healthy gait.

Results:
Compared with healthy participants, prosthesis users after OI surgery have slower speed and cadence, lower symmetry, longer duration of swing phase, increased pelvic and trunk motion, more hip extension, larger moments on the intact limb, and lower forces on the prosthetic side. Compared with transfemoral socket prosthesis gait, BAP gait shows faster cadence and longer duration of support phase. There are limited and inconsistent data on changes in trunk, pelvic, and hip motion with OI.

Conclusion:
Based on this review, transfemoral BAP improve spatial-temporal parameters closer to normal gait when compared to socket gait, but there are persisting deficits compared with healthy gait. Additional studies are needed to confirm the changes in kinematics and kinetics when walking with a BAP.
Long-Term Aesthetic Cicatrization Analysis of Lower Eyelid Incision for Orbital Floor Fracture Approach
Authors: Beneduce Nicola , Cassoni Andrea , Di Giorgio Danilo , Priore Paolo , Della Monaca Marco , Battisti Andrea , Valentini Valentino 
Published: August 2023

Orbital fractures are among the most frequent facial injuries. Of the 3 most widely described approaches in the literature, the lower eyelid approach is the authors’ preference. This study retrospectively analyzed the patients treated at the Trauma Center of the Umberto I Hospital, Sapienza University of Rome from January 2010 to December 2020.
Inclusion criteria were as follows: diagnosis of pure/impure orbital bone fracture, complete clinical and radiological documentation, and a minimum of 12 months follow-up. Sex, age, etiology, treatment, and associated complications were analyzed using IBM SPSS Statistics. Two internationally validated scales were used for the functional and esthetic long-term evaluation: the Patient and Observer Scar Assessment Scale (POSAS) and the Vancouver one. The scales were compiled by the patient himself and by 3 independent expert observers. Of the 543 patients who underwent surgery in the specified period, 208 fully met the inclusion criteria. One hundred forty-two (68.2%) were males and 66 (31.8%) were females, with a mean age of 40.68 years. The main cause was represented by assaults (33.1%). One hundred seventy-nine patients had a pure orbital fracture (83.8%) and 29 an impure one (16.2%). The most frequent symptoms at the time of diagnosis were diplopia (31.2%), followed by anesthesia of the second trigeminal branch (24.3%). Open reduction with internal fixation was the preferred treatment and proved to be effective in reducing the main signs and symptoms of the fracture in a statistically significant way (P < 0.05). Long-term esthetic results of the lower eyelid, using the Vancouver and POSASs, were respectively as follows: Vancouver Scar Scale mean total score was 2.41 (range: 0–8), observer POSAS mean total score was 1.83 (range: 1.2–3.9), observer general opinion mean score was 1.66, patient POSAS mean total score was 2.23 (range: 1.33–3.7), and patient general opinion mean score was 2.87.
The lower eyelid approach has proven to be reproducible, with a fast-learning curve and a low complication rate. The analysis conducted highlighted an excellent long-term esthetic-functional result. Further studies will be needed to statistically compare the results obtained with other orbital floor surgical approaches.
Sequencing of Physically Interacting Cells in Human Kidney Allograft Rejection to Infer Contact-dependent Immune Cell Transcription
Authors: Leckie-Harre Aidan , Silverman Isabel , Wu Haojia , Humphreys Benjamin D. , Malone Andrew F. 
Published: August 2023

Background.
Rejection requires cell–cell contact involving immune cells. Inferring the transcriptional programs of cell–cell interactions from single-cell RNA-sequencing (scRNA-seq) data is challenging as spatial information is lost.

Methods.
We combined a CD45pos enrichment strategy with Cellular Indexing of Transcriptomes and Epitopes by sequencing based quantification of leukocyte surface proteins to analyze cell–cell interactions in 11 human kidney transplant biopsies encompassing a spectrum of rejection diagnoses. scRNA-seq was performed using the 10X Genomics platform. We applied the sequencing physically interacting cells computational method to deconvolute the transcriptional profiles of heterotypic physically interacting cells.

Results.
The 11 human allograft biopsies generated 31 203 high-quality single-cell libraries. Clustering was further refined by combining Cellular Indexing of Transcriptomes and Epitopes by sequencing data from 6 different leukocyte-specific surface proteins. Three of 6 doublet clusters were identified as physically interacting cell complexes; macrophages or dendritic cells bound to B cells or plasma cells; natural killer (NK) or T cells bound to macrophages or dendritic cells and NK or T cells bound to endothelial cells. Myeloid-lymphocyte physically interacting cell complexes expressed activated and proinflammatory genes. Lymphocytes physically interacting with endothelial cells were enriched for NK and CD4 T cells. NK cell–endothelial cell contact caused increased expression of endothelial proinflammatory genes CXCL9 and CXCL10 and NK cell proinflammatory genes CCL3, CCL4, and GNLY.

Conclusions.
The transcriptional profiles of physically interacting cells from human kidney transplant biopsies can be inferred from scRNA-seq data using the sequencing physically interacting cells method. This approach complements previous methods that estimate cell–cell physical contact from scRNA-seq data.
Baseline and Serial BNP Measurements Predict Long-Term Mortality in Adults with Congenital Heart Disease: A study including 3,392 patients
Authors: Yumita Yusuke , Xu Zhuoyuan , Diller Gerhard-Paul , Kempny Aleksander , Rafiq Isma , Montanaro Claudia , Li Wei , Niwa Koichiro , Gu Hong , Dimopoulos Konstantinos , Gatzoulis Michael A , Brida Margarita 
Published: August 2023

AbstractBackgroundAlthough there is an ever growing number of adult patients with congenital heart disease (ACHD), many are still afflicted by premature death. Previous reports suggested that natriuretic peptides may identify ACHD patients with adverse outcome. We investigated the prognostic power of brain natriuretic peptide (BNP) across the spectrum of ACHD in a large contemporary cohort.MethodsWe retrospectively studied 3,392 consecutive and well-characterised ACHD patients under long-term follow-up at a tertiary ACHD centre between 2006-2019. The primary study endpoint was all-cause mortality.ResultsA total of 11,974 BNP measurements were analysed. The median BNP at baseline was 47 [24-107] ng/L. During a median follow-up of 8.6 years (29,115 patient-years), 615 (18.1%) patients died. On univariate and multivariate analysis both baseline BNP and temporal changes in BNP levels were predictive of mortality (p<0.001 for both) independent of congenital heart disease diagnosis, complexity, anatomic/haemodynamic features, and/or systolic systemic ventricular function. Patients within the highest quartile of baseline BNP (>107 ng/L) and those within the highest quartile of temporal BNP change (>35 ng/L) had 5.8 and 3.6-fold increased risk of death, respectively.ConclusionBaseline BNP and temporal BNP changes are both significantly associated with all-cause mortality in ACHD independent of congenital heart disease diagnosis, complexity, anatomic/haemodynamic features, and/or systolic systemic ventricular function. BNP levels represent an easy to obtain and inexpensive marker conveying prognostic information and should be used for the routine surveillance of patients with ACHD.
Comorbidity Profiles of Posttraumatic Stress Disorder Across the Medical Phenome
Authors: Hicks Emily M. , Niarchou Maria , Goleva Slavina , Kabir Dia , Ciarcia Julia ,   PTSD & Trauma EHR Working Group, Smoller Jordan W. , Davis Lea K. , Nievergelt Caroline M. , Koenen Karestan C. , Huckins Laura M. , Choi Karmel W. 
Published: August 2023

AbstractBackgroundPrior epidemiological research has linked PTSD with specific physical health problems, but the comprehensive landscape of medical conditions associated with PTSD remains uncharacterized. Electronic health records (EHR) provide an opportunity to overcome prior clinical knowledge gaps and uncover associations with biological relevance that potentially vary by sex.MethodsPTSD was defined among biobank participants (total N=123,365) in a major healthcare system using two ICD code-based definitions: broad (1+ PTSD or acute stress codes versus 0; NCase=14,899) and narrow (2+ PTSD codes versus 0; NCase=3,026). Using a phenome-wide association (PheWAS) design, we tested associations between each PTSD definition and all prevalent disease umbrella categories, i.e., phecodes. We also conducted sex-stratified PheWAS analyses including a sex-by-diagnosis interaction term in each logistic regression.ResultsA substantial number of phecodes were significantly associated with PTSDNarrow(61%) and PTSDBroad(83%). While top associations were shared between the two definitions, PTSDBroadcaptured 334 additional phecodes not significantly associated with PTSDNarrowand exhibited a wider range of significantly associated phecodes across various categories, including respiratory, genitourinary, and circulatory conditions. Sex differences were observed, in that PTSDBroadwas more strongly associated with osteoporosis, respiratory failure, hemorrhage, and pulmonary heart disease among male patients, and with urinary tract infection, acute pharyngitis, respiratory infections, and overweight among female patients.ConclusionsThis study provides valuable insights into a diverse range of comorbidities associated with PTSD, including both known and novel associations, while highlighting the influence of sex differences and the impact of defining PTSD using EHR.
Sex differences in the pleiotropy of hearing difficulty with imaging-derived phenotypes: a brain-wide investigation
Authors: He Jun , Cabrera-Mendoza Brenda , Angelis Flavio De , Pathak Gita A. , Koller Dora , Curhan Sharon G. , Curhan Gary C. , Mecca Adam P. , van Dyck Christopher H. , Polimanti Renato 
Published: August 2023

ABSTRACTBackgroundHearing difficulty (HD) is one of the major health burdens in older adults. While aging-related changes in the peripheral auditory system play an important role, genetic variation associated with brain structure and function could also be involved in HD predisposition.MethodsWe analyzed a large-scale HD genome-wide association study (GWAS; Ntotal= 501,825, 56% females) and GWAS data related to 3,935 brain imaging-derived phenotypes (IDPs) assessed in up to 33,224 individuals (52% females) using multiple magnetic resonance imaging (MRI) modalities. To investigate HD pleiotropy with brain structure and function, we conducted genetic correlation, latent causal variable (LCV), Mendelian randomization (MR), and multivariable generalized linear regression analyses. Additionally, we performed local genetic correlation and multi-trait colocalization analyses to identify genomic regions and loci implicated in the pleiotropic mechanisms shared between HD and brain IDPs.ResultsWe observed a widespread genetic correlation of HD with 120 IDPs in females, 89 IDPs in males, and 171 IDPs in the sex-combined analysis. The LCV analyses showed that some of these genetic correlations could be due to cause-effect relationships. For seven correlations, the causal effects were also confirmed by the MR approach: vessel volume→HD in the sex-combined analysis; hippocampus volume→HD, cerebellum grey matter volume→HD, primary visual cortex volume→HD, and HD→rfMRI-ICA100 node 46 in females; global mean thickness→HD and HD→mean orientation dispersion index in superior corona radiata in males. The local genetic correlation analyses identified 13 pleiotropic regions between HD and these seven IDPs. We also observed a colocalization signal for the rs13026575 variant between HD, primary visual cortex volume, andSPTBN1transcriptomic regulation in females.ConclusionBrain structure and function may have a role in the sex differences in HD predisposition via possible cause-effect relationships and shared regulatory mechanisms.
Glioblastoma-infiltrating CD8+T cells are predominantly a clonally expandedGZMK+effector population
Authors: Wang Anthony Z. , Mashimo Bryce L. , Schaettler Maximilian O. , Sherpa Ngima D. , Leavitt Lydia A. , Livingstone Alexandra J. , Khan Saad M. , Li Mao , Anzaldua-Campos Markus , Bradley Joseph D. , Leuthardt Eric C. , Kim Albert H. , Dowling Joshua L. , Chicoine Michael R. , Jones Pamela S. , Choi Bryan D. , Cahill Daniel P. , Carter Bob S. , Petti Allegra A. , Johanns Tanner M. , Dunn Gavin P. 
Published: August 2023

AbstractRecent clinical trials have highlighted the limited efficacy of T cell-based immunotherapy in patients with glioblastoma (GBM). To better understand the characteristics of tumor-infiltrating lymphocytes (TIL) in GBM, we performed cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and single-cell RNA sequencing (scRNA-seq) with paired V(D)J sequencing, respectively, on TIL from two cohorts of patients totaling 15 patients with high grade glioma, including GBM or astrocytoma, IDH mutant, grade 4 (G4A). Analysis of the CD8+TIL landscape reveals an enrichment of clonally expandedGZMK+effector T cells in the tumor compared to matched blood, which was validated at the protein level. Furthermore, integration with other cancer types highlights the lack of a canonically exhausted CD8+T cell population in GBM TIL. These data suggest thatGZMK+effector T cells represent an important T cell subset within the GBM microenvironment and which may harbor potential therapeutic implications.SignificanceIn order to understand the limited efficacy of immune checkpoint blockade in GBM, we endeavor to understand the TIL landscape through a multi-omics approach. In this study, by highlighting the enrichment ofGZMK+effector T cells and lack of exhausted T cells, we provide a new potential mechanism of resistance to immunotherapy in GBM.
Combined topological data analysis and geometric deep learning reveal niches by the quantification of protein binding pockets
Authors: Jiang Peiran , Lugo-Martinez Jose 
Published: August 2023

ABSTRACTProtein pockets are essential for many proteins to carry out their functions. Locating and measuring protein pockets as well as studying the anatomy of pockets helps us further understand protein function. Most research studies focus on learning either local or global information from protein structures. However, there is a lack of studies that leverage the power of integrating both local and global representations of these structures. In this work, we combine topological data analysis (TDA) and geometric deep learning (GDL) to analyze the putative protein pockets of enzymes. TDA captures blueprints of the global topological invariant of protein pockets, whereas GDL decomposes the fingerprints to building blocks of these pockets. This integration of local and global views provides a comprehensive and complementary understanding of the protein structural motifs (nichesfor short) within protein pockets. We also analyze the distribution of the building blocks making up the pocket and profile the predictive power of coupling local and global representations for the task of discriminating between enzymes and non-enzymes. We demonstrate that our representation learning framework for macromolecules is particularly useful when the structure is known, and the scenarios heavily rely on local and global information.
HER2 overexpression initiates breast tumorigenesis non-cell-autonomously by inducing oxidative stress in the tissue microenvironment
Authors: Gurler Sevim B. , Wagstaff Oliver , Dimitrova Lili , Chen Fuhui , Pedley Robert , Weston William , Donaldson Ian J. , Telfer Brian A. , Novo David , Pavlou Kyriaki , Taylor George , Ou Yaqing , Williams Kaye J. , Gilmore Andrew , Brennan Keith , Ucar Ahmet 
Published: August 2023

SUMMARYHER2 is considered as a driver oncogene responsible for the HER2+ subtype of breast cancer. However, it is still unclear how HER2 induces the oncogenic transformation of breast cancer stem cells (BCSCs) and initiates tumorigenesis during premalignant stage breast cancer. Here, we used clinical samples and mouse models of HER2+ breast cancer to demonstrate that neither BCSCs nor their cell-of-origin express HER2/Neu in early-stage breast tumors. Instead, our results demonstrate that Neu overexpression results in the transformation of BCSCs in a non-cell-autonomous manner via triggering DNA damage and somatic mutagenesis in their Neu-negative cell-of-origin. This is caused by the increased oxidative stress in the tissue microenvironment generated by altered energy metabolism and increased reactive oxygen species levels in Neu-overexpressing mammary ducts. Therefore, our findings illustrate a previously unrecognized mechanism of HER2-induced breast tumor initiationin vivowith potential impacts on future preventive treatments for HER2+ premalignant breast cancer.
Neural correlates of aggression outcome expectation and their association with aggression: A voxel-based morphometry study
Authors: Gong Xinyu , Hu Bohua , Wang Liang , He Qinghua , Xia Ling-Xiang 
Published: August 2023

AbstractBackgroundThe aggression outcome expectation is believed to be an important cognitively influencing factor of aggression. Discovering the neural mechanism of aggression outcome expectation is conductive to develop aggression research. However, the neural correlates underlying aggression outcome expectation and its deleterious effect remain elusive.MethodsIn this study, we utilized voxel-based morphometry (VBM) to unravel the neural architecture of aggression outcome expectation measured by the Social Emotional Information Processing Assessment for Adults and and its relationship with aggression measured by the Buss Perry Aggression Questionnaire in a sample of 185 university students (114 female; mean age = 19.94 ± 1.62 years; age range: 17-32 years).ResultsThe results showed a significantly positive correlation between aggression outcome expectation and the regional gray matter volume (GMV) in the right middle temporal gyrus (MTG) (x = 55.5, y = -58.5, z = 1.5; t =3.35; cluster sizes =352,p< 0.05, GRF corrected). Moreover, aggression outcome expectation acted as a mediator underlying the association between the right MTG volume and aggression.ConclusionsThese results found the neural correlates of aggression outcome expectation and its effect on aggression for the first time, which may contribute to our understanding of the cognitive neural mechanism of aggression and tentatively provide an effective method to identify potential neurobiological markers for aggression.
Prevalence of somatosensory modulation of the cervical spine and temporomandibular joint in subjects with tinnitus: a systematic review
Authors: Segreto Marco , Giusti Andrea , Bizzarri Paolo 
Published: August 2023

ABSTRACTBackgroundTinnitus is defined as the perception of a sound without a corresponding external acoustic stimulus and is considered a symptom rather than a disease. In some individuals, it can be evoked or modulated by input from the somatosensory, somatomotor, and visual-motor systems. This has led to the introduction of the term: ‘‘somatosensory modulation of tinnitus’’. In these cases, the psychoacoustic attributes of tinnitus (loudness and pitch) can change as a result of external stimuli such as strong contractions of the muscles of the head, neck, limbs, orofacial movements, and eye movements. The temporomandibular joint and cervical spine, along with the head, appear to be the musculoskeletal anatomical regions most commonly underlying somatic tinnitus. This review aims to evaluate the prevalence of somatosensory modulation of the cervical spine and temporomandibular joint in subjects with tinnitus.MethodsThe databases investigated for the review were: Embase, Pubmed, Scopus, and Web of Science. Observational studies investigating the prevalence of somatosensory modulation of the cervical spine and temporomandibular joint in subjects with tinnitus were included. No time limit was entered into the search and no age or language restrictions were applied.Results14 studies met the eligibility criteria on which the review was based. In 5 studies, the prevalence of tinnitus modulation was reported with one or more maneuvers involving TMJ, in 3 studies with one or more maneuvers involving the cervical spine and 7 studies reported the prevalence of modulation following maneuvers for both somatic regions.ConclusionThe present study confirmed that tinnitus perception and intensity can be somatically modulated in a subpopulation of individuals. The cervical spine and the ATM play a key role in the modulation of tinnitus and, based on the data collected on individual districts, the ATM appears to be the most frequently involved somatic region.
The Impact of Laterality on the Incidence and Prognosis of Epithelial Ovarian Cancer
Authors: Zhang Yang , Huang Yucong , Kang Jihui , Yao Shuzhong , Gu Langyu , Yang Guofen 
Published: August 2023

AbstractEpithelial ovarian cancer (EOC) is the most common type of ovarian cancer, and its mortality rate is the highest among gynecological malignancies. Despite numerous factors being linked to the prognosis of EOC, the impact of ovarian laterality has received limited attention. In this study, we comprehensively examined the effects of laterality (left-right and bilateral-unilateral) on the incidence and prognosis of EOC, with a particular focus on different subtypes. By utilizing a large clinical database, we found that laterality differences primarily existed between unilateral and bilateral cases in terms of both incidence and prognosis. Specifically, unilateral tumour development was predominantly observed in patients with clear cell, endometrioid, and mucinous ovarian cancer subtypes, while bilateral involvement was more common in serous ovarian cancer. Laterality differences, reflecting disparities between the left and right sides, were primarily observed in various stages of the overall population and within specific EOC subtypes. Specifically, significant differences in EOC incidence between the left and right sides at different stages were observed in the overall population, as well as in clear cell, endometrioid, and serous ovarian cancer subtypes. Although no significant differences in the incidence rate between the left and right sides were noted for mucinous ovarian cancer, the prognosis was substantially better on the right side compared to the left side. These findings underscore the importance of considering ovarian laterality, both in terms of left-right and bilateral-unilateral aspects, as a critical factor associated with the incidence and prognosis of EOC. Therefore, it should be taken into account in clinical practice, particularly in the context of different tumour stages and subtypes of EOC.