bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrasonographic Features of Trigger Finger in Patients With Hyperuricemia
Authors: Wang Ping-Hui , Hsieh Tai-Jung , Wu Tung-Tai , Wu Kuo-Chen , Jou I-Ming 
Published: October 2019

Purpose
The purpose of the current study was to compare demographic differences and ultrasonographic features in primary trigger finger and trigger finger in association with hyperuricemia.

Methods
Between October 2008 and February 2010, a prospective review of consecutive cases of 54 patients with trigger finger and hyperuricemia, 76 patients with a trigger finger without hyperuricemia, and 80 control cases were enrolled. The clinical results were analyzed by descriptive epidemiology, an ultrasonographic measurement of the thickness of A1 pulley, cross-sectional area of the flexor tendon and synovium.

Results
The middle finger was primarily affected, followed by the index and ring fingers in both trigger finger groups. The thickness of A1 pulley, cross-sectional area of the flexor tendon, and flexor tendon with synovium in trigger finger without hyperuricemia group were significantly larger than that in trigger finger with hyperuricemia and control groups. There was no significant difference between trigger finger with hyperuricemia and control groups. Double-contour sign and tophus were only observed in trigger finger with hyperuricemia group.

Conclusions
Thickness of A1 pulley, cross-sectional area of the flexor tendon, and flexor tendon with synovium were significantly larger in trigger finger without hyperuricemia group. These findings were not evident in trigger finger with hyperuricemia group.
Virtual Surgical Planning for Mandibular Reconstruction With the Fibula Free Flap
Authors: Barr Meaghan L. , Haveles Christos S. , Rezzadeh Kameron S. , Nolan Ian T. , Castro Ruben , Lee Justine C. , Steinbacher Derek , Pfaff Miles J. 
Published: October 2019

Background
The fibula free flap (FFF) remains the criterion standard for complex mandibular reconstruction. Surgeons have incorporated virtual surgical planning (VSP) into the reconstructive algorithm with the assertion that VSP increases operative efficiency and may improve clinical outcomes. To date, no large-scale studies have analyzed these claims. This study examines the literature and tests the hypothesis that VSP improves operative efficiency, clinical outcomes, and accuracy when compared with traditional techniques.

Methods
A systematic review was performed to identify articles utilizing VSP and traditional techniques for FFF-based mandibular reconstruction. Two reviewers independently assessed all articles for methodological quality using a validated instrument (weighted Cohen κ for interrater reliability = 0.70). Outcomes included operative time, length of stay, complications, and accuracy. Meta-analytic comparisons were performed using data from comparative studies using a random-effects model and differences of means analysis for outcomes measured on identical scales.

Results
One hundred thirty-one articles were identified, and 25 met the inclusion criteria: 12 were VSP only, whereas 13 were comparative. There were 241 VSP patients and 214 traditional patients available for meta-analysis. Patients undergoing reconstruction with VSP had a significant reduction in operative time by 44.64 minutes (95% confidence interval [CI], −74.69 to −14.58 minutes; P < 0.01) and demonstrated a mean trend toward shorter hospital admission (mean difference, −1.24 days; 95% CI, −4.00 to 1.52 days; P = 0.38). There was no statistical difference between cohorts for major (odds ratio, 1.03; 95% CI, 0.46–2.31; P = 0.95) or minor complications (odds ratio, 0.97; 95% CI, 0.54–1.71; P = 0.90). Insufficient data were available for cost analysis and accuracy.

Conclusions
Virtual surgical planning–guided mandibular reconstruction with FFF is associated with significantly decreased operative time and a mean trend toward shorter hospital admission. While multiple studies reported a high degree of accuracy, no standard measurement was available for meta-analysis.
Deep Inferior Epigastric Perforator Breast Reconstruction With Computer-Aided Design/Computer-Aided Manufacturing Sizers
Authors: Gelati Chiara , Lozano Miralles Maria Elisa , Morselli Paolo Giovanni , Fabbri Erich , Cipriani Riccardo 
Published: October 2019

Background
The goal of microsurgical breast reconstruction is to return to the precancer state, maximizing symmetry with less morbidity. This requires a long learning curve, in particular where modeling is concerned. In this context, reverse engineering technologies found an application, allowing the creation of molds that can be used during the surgery.

Method
We created 10 molds named DIEP sizers, which help to simplify deep inferior epigastric perforator (DIEP) flap insetting. For this, we designed a virtual model using Geomagic X software to construct the sizers. Our model has a thorax circumference, breast projection, and footprint correspondent to an average of the measurements we collected from 15 patients undergoing such surgery. We made a comparative study between 2 groups each of 24 patients, using as comparison criteria surgical times in patients undergoing breast microsurgical reconstruction with or without DIEP sizers. In both groups, we included immediate and delayed reconstructions as well as monolateral, bilateral and monolateral with contralateral symmetrization.

Result
In all the cases we performed with DIEP sizers, we achieved an average time saving of 105 minutes in monolateral reconstruction, 80 minutes in monolateral reconstruction with contralateral symmetrization, and 120 minutes in bilateral reconstruction (P < 0.001). No major complications occurred.

Conclusions
We performed 24 breast reconstructions with preformed molds, obtaining a proper “library” with different DIEP sizers that can be used both in preoperative planning and in intraoperative modeling. We recommend the use of a preformed mold in microsurgical breast reconstruction to improve symmetry, to shorten the learning curve and to save time.
Assessment of Clinical and Histological Changes in the Skin Paddle of Pectoralis Major Myocutaneous Flap in Intraoral Reconstruction
Authors: Behera Saswati , Mohsina Subair , Tripathy Satyaswarup , John Jerry R. , Sharma Ramesh Kumar , Panda Naresh Kumar , Bakshi Jaimanti , Radotra Bishan Dass , Sahu Ranjit Kumar 
Published: October 2019

Purpose
This study was carried out to characterize the clinical and histological changes in the cutaneous portion of the transferred pedicled pectoralis major myocutaneous flaps used in intraoral reconstruction in patients with head and neck malignancy.

Methods
This was a prospective cohort study carried out from July 2016 to 2018. All patients underwent ablative surgery for oropharyngeal cancers and primary reconstruction with pedicled pedicled pectoralis major myocutaneous flaps. The intraoral flaps were examined for color, texture, presence of hair, chronic inflammatory changes, and ulceration. At 12 months, incisional biopsies were taken from the skin paddle of the intraoral flap and contralateral normal buccal mucosa, and flap histology was compared with that of the contralateral buccal mucosa.

Results
Twenty patients were included in the final analysis (M/F, 4:1; mean ± SD age, 51.38 ± 6.76 years). Fourteen flaps resembled oral mucosa, 3 had a mixed appearance of both skin and mucosa, and 3 had appearance of normal skin at 1 year follow-up. The epidermis and stratum corneum were retained in all the flap biopsies; however, severe attenuation was noted in 7 patients (had mucosal appearance) but was significantly different from oral mucosa(P = 0.0003). Cutaneous appendages were found in all the flap epithelia. Thirteen flaps showed grossly attenuation, of which 11 patients had a gross appearance resembling oral mucosa and 2 had a mixed appearance. The biopsies showed varied degree of chronic changes like desquamation in around 35% (7 patients), hyperkeratosis in 35% (7 patients), and chronic candidiasis in 30% (6 patients).

Conclusions
Although the intraorally transferred flaps demonstrate a morphological appearance similar to oral mucosa, there is a histological preservation of skin elements and architecture.
Surgical Treatment of Mandible Fracture Using Unsintered Hydroxyapatite/Poly l-Lactide Composite Fixation System
Authors: Lee Sun Jae , Park Eun Soo , Nam Seung Min , Choi Chang Yong , Shin Ho Sung , Kim Yong Bae 
Published: October 2019

Abstract
Recently, absorbable plates have been used for various types of facial fractures. However, in the case of mandibular fractures, a large amount of force is applied after fixation. Thus, a firm fixation is necessary. In particular, unfavorable fractures are more frequent in mandibular fractures. Therefore, plates should be strong enough to withstand forces at the time of surgery. The purpose of this study was to determine clinical efficacy and usefulness of unsintered hydroxyapatite (u-HA)/poly (l-lactide) (PLLA) composite system by clinical application and follow-up of fixation in patients with mandible fracture. A total of 13 patients with mandible fractures were assessed for compliance with the selection criteria. Fracture site was confirmed with radiographic findings including X-ray and facial computed tomography images. Subjects who fulfilled all criteria underwent operation using HA/PLLA composite fixation system (OSTEOTRANS; Takiron Co Ltd, Osaka, Japan). After reduction of fracture site through oral or skin incision, we placed OSTEOTRANS plates on fracture line and performed rigid fixation with OSTEOTRANS-MX screws. Follow-up was performed at 1 week, 1, 3, and 6 months after surgery. Occlusion and mouth opening were checked by physical examination and radiographic finding. We also confirmed bone approximation status, bony gap change, and bone union status. All patients finished every follow-up. They were satisfied with outcomes without complications such as malocclusion, foreign body sensation, or tenderness. This study confirms that OSTEOTRANS can be used appropriately for mandibular fractures.
Bringing Proportional Recovery into Proportion: Bayesian Hierarchical Modelling of Post-Stroke Motor Performance
Authors: Bonkhoff Anna K. , Hope Thomas , Bzdok Danilo , Guggisberg Adrian G. , Hawe Rachel L. , Dukelow Sean P. , Rehme Anne K. , Fink Gereon R. , Grefkes Christian , Bowman Howard 
Published: October 2019

AbstractAccurate predictions of motor performance after stroke are of cardinal importance for the patient, clinician, and health care system. More than ten years ago, the proportional recovery rule was introduced by promising just that: high-fidelity predictions of recovery following stroke based only on the initially lost motor performance, at least for a specific fraction of patients. However, emerging evidence suggests that this recovery rule is subject to various confounds and may apply less universally than assumed by many.We systematically revisited stroke outcome predictions by casting the data in a less confounded form and employing more integrative and flexible hierarchical Bayesian models. We jointly analyzedn=385 post-stroke trajectories from six separate studies – the currently largest overall dataset of upper limb motor recovery. We addressed confounding ceiling effects by introducing a subset approach and ensured correct model estimation through synthetic data simulations. Finally, we used model comparisons to assess the underlying nature of recovery within our empirical recovery data.The first model comparison, relying on the conventional fraction of patients calledfitters, pointed to a combination of constant and proportional to lost function recovery. Proportional to lost here describes the original notion of proportionality, indicating greater recovery in case of a more pronounced initial deficit. This combination explained only 32% of the variance in recovery, which is in stark contrast to previous reports of >80%. When instead analyzing the complete spectrum of subjects, model comparison selected a composite of constant and proportional to spared function recovery, implying a more significant improvement in case of more preserved function. Explained variance was at 53%.Therefore, our data suggest that motor recovery post-stroke may exhibit some characteristics of proportionality. However, the levels of explanatory value were substantially reduced compared to what has previously been reported. This finding motivates future research moving beyond solely behavior scores to explain stroke recovery and establish robust single-subject predictions.
Fluorescence and light scatter calibration allow comparisons of small particle data in standard units across different flow cytometry platforms and detector settings
Authors: Welsh J.A. , Jones J.C. , Tang V.A. 
Published: October 2019

AbstractFlow cytometers have been utilized for the analysis of submicron-sized particles since the late 1970s. Initially, virus analyses preceded extracellular vesicle (EV), which began in the 1990s. Despite decades of documented use, the lack of standardization in data reporting has resulted in a growing body of literature that cannot be easily interpreted, validated, or reproduced. This has made it difficult for objective assessments of both assays and instruments, in-turn leading to significant hindrances in scientific progress, specifically in the study of EVs, where the phenotypic analysis of these submicron-sized vesicles is becoming common-place in every biomedical field. Methods for fluorescence and light scatter standardization are well established and the reagents to perform these analyses are commercially available. However, fluorescence and light scatter calibration are not widely adopted by the small particle community as methods to standardize flow cytometry data. In this proof-of-concept study carried out as a resource for use at the CYTO2019 workshop, we demonstrate for the first-time simultaneous fluorescence and light scatter calibration of small particle data to show the ease and feasibility of this method for standardized flow cytometry data reporting. This data was acquired using standard configuration commercial flow cytometers, with commercially available materials, published methods, and freely available software tools. We show that application of light scatter, fluorescence, and concentration calibration can result in highly concordant data between flow cytometry platforms independent of instrument collection angle, gain/voltage settings, and flow rate; thus, providing a means of cross-comparison in standard units.
Personalized Network Modeling of the Pan-Cancer Patient and Cell Line Interactome
Authors: Bhattacharyya Rupam , Ha Min Jin , Liu Qingzhi , Akbani Rehan , Liang Han , Baladandayuthapani Veerabhadran 
Published: October 2019

ABSTRACTPurposePersonalized network inference on diverse clinical andin vitromodel systems across cancer types can be used to delineate specific regulatory mechanisms, uncover drug targets and pathways, and develop individualized predictive models in cancer.Datasets and methodsWe developed TransPRECISE, a multi-scale Bayesian network modeling framework, to analyze the pan-cancer patient and cell line interactome to identify differential and conserved intra-pathway activities, globally assess cell lines as representative models for patients and develop drug sensitivity prediction models. We assessed pan-cancer pathway activities for a large cohort of patient samples (>7700) from The Cancer Proteome Atlas across ≥30 tumor types and a set of 640 cancer cell lines from the M.D. Anderson Cell Lines Project spanning16 lineages, and ≥250 cell lines’ response to >400 drugs.ResultsTransPRECISE captured differential and conserved proteomic network topologies and pathway circuitry between multiple patient and cell line lineages: ovarian and kidney cancers shared high levels of connectivity in the hormone receptor and receptor tyrosine kinase pathways, respectively, between the two model systems. Our tumor stratification approach found distinct clinical subtypes of the patients represented by different sets of cell lines: head and neck patient tumors were classified into two different subtypes that are represented by head and neck and esophagus cell lines, and had different prognostic patterns (456 vs. 654 days of median overall survival; P=0.02). The TransPRECISE-based sample-specific pathway scores achieved high predictive accuracy for drug sensitivities in cell lines across multiple drugs (median AUC >0.8).ConclusionOur study provides a generalizable analytical framework to assess the translational potential of preclinical model systems and guide pathway-based personalized medical decision-making, integrating genomic and molecular data across model systems.
The cryo-EM structure of the bacterial flagellum cap complex suggests a molecular mechanism for filament elongation
Authors: Al-Otaibi Natalie S. , Taylor Aidan J. , Farrell Daniel P. , Tzokov Svetomir B. , DiMaio Frank , Kelly David J. , Bergeron Julien R.C. 
Published: October 2019

AbstractThe bacterial flagellum is a remarkable molecular motor, present at the surface of many bacteria, whose primary function is to allow motility through the rotation of a long filament protruding from the bacterial cell. A cap complex, consisting of an oligomeric assembly of the protein FliD, is localized at the tip of the flagellum, and is essential for filament assembly, as well as adherence to surfaces in some bacteria. However, the structure of the intact cap complex, and the molecular basis for its interaction with the filament, remains elusive. Here we report the cryo-EM structure of the Campylobacter jejuni cap complex. This structure reveals that FliD is pentameric, with the N-terminal region of the protomer forming an unexpected extensive set of contacts across several subunits, that contribute to FliD oligomerization. We also demonstrate that the native C. jejuni flagellum filament is 11-stranded and propose a molecular model for the filament-cap interaction.
A Brain to Spine Interface for Transferring Artificial Sensory Information
Authors: Yadav Amol P. , Li Daniel , Nicolelis Miguel A. L. 
Published: October 2019

AbstractLack of sensory feedback is a major obstacle in the rapid absorption of prosthetic devices by the brain. While electrical stimulation of cortical and subcortical structures provides unique means to deliver sensory information to higher brain structures, these approaches require highly invasive surgery and are dependent on accurate targeting of brain structures. Here, we propose a semi-invasive method, Dorsal Column Stimulation (DCS) as a tool for transferring sensory information to the brain. Using this new approach, we show that rats can learn to discriminate artificial sensations generated by DCS and that DCS-induced learning results in corticostriatal plasticity. We also demonstrate a proof of concept brain-to-spine interface (BTSI), whereby tactile and artificial sensory information are decoded from the brain of an “encoder” rat, transformed into DCS pulses, and delivered to the spinal cord of a second “decoder” rat while the latter performs an analog-to-digital conversion during a tactile discrimination task. These results suggest that DCS can be used as an effective sensory channel to transmit prosthetic information to the brain or between brains, and could be developed as a novel platform for delivering tactile and proprioceptive feedback in clinical applications of brain-machine interfaces.
An ecophysiological model of plant-pest interactions: the role of nutrient and water availability
Authors: Zaffaroni Marta , Cunniffe Nik J. , Bevacqua Daniele 
Published: October 2019

AbstractEmpirical studies have shown that particular irrigation/fertilization regimes can control pest populations in agroecosystems. This appears to promise that the ecological concept of bottom-up control can be applied to pest management. However, a conceptual framework is necessary to develop a mechanistic basis for empirical evidence. Here we couple a mechanistic plant growth model with a pest population model. We demonstrate its utility by applying it to the peach - green aphid system. Aphids are herbivores which feed on the plant phloem, deplete plants’ resources and (potentially) transmit viral diseases. The model reproduces system properties observed in field studies and shows under which conditions the diametrically-opposed plant vigour and plant stress hypotheses find support. We show that the effect of fertilization/irrigation on the pest population cannot be simply reduced as positive or negative. In fact, the magnitude and direction of any effect depends on the precise level of fertilization/irrigation and on the date of observation. We show that a new synthesis of experimental data can emerge by embedding a mechanistic plant growth model, widely studied in agronomy, in a consumer-resource modelling framework, widely studied in ecology. The future challenge is to use this insight to inform practical decision making by farmers and growers.
Identification of putative effector genes across the GWAS Catalog using molecular quantitative trait loci from 68 tissues and cell types
Authors: Guo Cong , Sieber Karsten B. , Esparza-Gordillo Jorge , Hurle Mark R. , Song Kijoung , Yeo Astrid J. , Yerges-Armstrong Laura M. , Johnson Toby , Nelson Matthew R. 
Published: October 2019

AbstractIdentifying the effector genes from genome-wide association studies (GWAS) is a crucial step towards understanding the biological mechanisms underlying complex traits and diseases. Colocalization of expression and protein quantitative trait loci (eQTL and pQTL, hereafter collectively called “xQTL”) can be effective for mapping associations to genes in many loci. However, existing colocalization methods require full single-variant summary statistics which are often not readily available for many published GWAS or xQTL studies. Here, we present PICCOLO, a method that uses minimum SNP p-values within a locus to determine if pairs of genetic associations are colocalized. This method greatly expands the number of GWAS and xQTL datasets that can be tested for colocalization. We applied PICCOLO to 10,759 genome-wide significant associations across the NHGRI-EBI GWAS Catalog with xQTLs from 28 studies. We identified at least one colocalized gene-xQTL in at least one tissue for 30% of associations, and we pursued multiple lines of evidence to demonstrate that these mappings are biologically meaningful. PICCOLO genes are significantly enriched for biologically relevant tissues, and 4.3-fold enriched for targets of approved drugs.