bluuebunny/crossref_metadata_2025_split huggingface dataset:
A simple linear model to aid in analyses of the β Pictoris moving group
Authors: Barbosa Valmir C , do Nascimento Josina O 
Published: November 2022

ABSTRACT
We build a 4D linear model of object membership in the $\beta$ Pictoris moving group (BPMG), using two nested applications of Principal Component Analysis (PCA) for ∼1.5 million objects with high-quality data. These data consist of 3D-Galactic space velocities and Gaia G magnitudes. Through PCA, they ultimately result in a 4D straight line, referred to as PC 1′, about which both the bona fide members used to obtain the straight line and the candidate members used to test the model congregate at generally small distances. As a proof of concept, we select bona fide members from a recent, Gaia DR2-based compilation and candidate members mostly from a (pre-Gaia DR2) compilation from 2017. Using a standard procedure to flag groups of outliers in data sets, we find possible outliers flagged on account of their large distances to PC 1′, and find evidence that discrepant radial velocity measurements may indeed bring into question their validity as BPMG members. We propose that PC 1′ be added to the tool set for BPMG analyses and potentially extended to other young stellar moving groups.
SirA inhibits the essential DnaA:DnaD interaction to block helicase recruitment duringBacillus subtilissporulation
Authors: Winterhalter Charles , Stevens Daniel , Fenyk Stepan , Pelliciari Simone , Marchand Elie , Soultanas Panos , Ilangovan Aravindan , Murray Heath 
Published: November 2022

AbstractBidirectional DNA replication from a chromosome origin requires the asymmetric loading of two helicases, one for each replisome. Our understanding of the molecular mechanisms underpinning helicase loading at bacterial chromosome origins is incomplete. Here we report both positive and negative mechanisms for directing helicase recruitment in the model organism Bacillus subtilis. Systematic characterization of the essential initiation protein DnaD revealed distinct protein interfaces required for homo-oligomerization, interaction with the master initiator protein DnaA, and interaction with the helicase co-loader protein DnaB. Informed by these properties of DnaD, we went on to find that the developmentally expressed repressor of DNA replication initiation, SirA, blocks the interaction between DnaD and DnaA, thereby restricting helicase recruitment from the origin during sporulation to inhibit further initiation events. These results advance our understanding of the mechanisms underpinning DNA replication initiation in B. subtilis, as well as guiding the search for essential cellular activities to target for antimicrobial drug design.
MobiDB: 10 years of intrinsically disordered proteins
Authors: Piovesan Damiano , Del Conte Alessio , Clementel Damiano , Monzon Alexander Miguel , Bevilacqua Martina , Aspromonte Maria Cristina , Iserte Javier A , Orti Fernando E , Marino-Buslje Cristina , Tosatto Silvio C E 
Published: November 2022

AbstractThe MobiDB database (URL: https://mobidb.org/) is a knowledge base of intrinsically disordered proteins. MobiDB aggregates disorder annotations derived from the literature and from experimental evidence along with predictions for all known protein sequences. MobiDB generates new knowledge and captures the functional significance of disordered regions by processing and combining complementary sources of information. Since its first release 10 years ago, the MobiDB database has evolved in order to improve the quality and coverage of protein disorder annotations and its accessibility. MobiDB has now reached its maturity in terms of data standardization and visualization. Here, we present a new release which focuses on the optimization of user experience and database content. The major advances compared to the previous version are the integration of AlphaFoldDB predictions and the re-implementation of the homology transfer pipeline, which expands manually curated annotations by two orders of magnitude. Finally, the entry page has been restyled in order to provide an overview of the available annotations along with two separate views that highlight structural disorder evidence and functions associated with different binding modes.
High-affinity binding at quadruplex–duplex junctions: rather the rule than the exception
Authors: Vianney Yoanes Maria , Weisz Klaus 
Published: November 2022

Abstract
Quadruplex-duplex (Q–D) junctions constitute unique structural motifs in genomic sequences. Through comprehensive calorimetric as well as high-resolution NMR structural studies, Q–D junctions with a hairpin-type snapback loop coaxially stacked onto an outer G-tetrad were identified to be most effective binding sites for various polycyclic quadruplex ligands. The Q–D interface is readily recognized by intercalation of the ligand aromatic core structure between G-tetrad and the neighboring base pair. Based on the thermodynamic and structural data, guidelines for the design of ligands with enhanced selectivity towards a Q–D interface emerge. Whereas intercalation at Q–D junctions mostly outcompete stacking at the quadruplex free outer tetrad or intercalation between duplex base pairs to varying degrees, ligand side chains considerably contribute to the selectivity for a Q–D target over other binding sites. In contrast to common perceptions, an appended side chain that additionally interacts within the duplex minor groove may confer only poor selectivity. Rather, the Q–D selectivity is suggested to benefit from an extension of the side chain towards the exposed part of the G-tetrad at the junction. The presented results will support the design of selective high-affinity binding ligands for targeting Q–D interfaces in medicinal but also technological applications.
Comprehensive profiling of epigenetic modifications in fast-growing Moso bamboo shoots
Authors: Li Tao , Wang Huihui , Zhang Yaxin , Wang Huiyuan , Zhang Zeyu , Liu Xuqing , Zhang Zekun , Liu Kai , Yang Deming , Zhang Hangxiao , Gu Lianfeng 
Published: November 2022

Abstract
The fast growth of Moso bamboo (Phyllostachys edulis) shoots is caused by the rapid elongation of each internode. However, the key underlying cellular processes and epigenetic mechanisms remain largely unexplored. We used microscopy and multi-omics approaches to investigate two regions (bottom and middle) of the 18th internode from shoots of two different heights (2 and 4 m). We observed that internode cells become longer, and that lignin biosynthesis and glycosyltransferase family 43 (GT43) genes are substantially upregulated with shoot height. Nanopore direct RNA sequencing (DRS) revealed a higher N6-methyladenine (m6A) modification rate in 2-m shoots than in 4-m shoots. In addition, different specific m6A modification sites were enriched at different growth stages. Global DNA methylation profiling indicated that DNA methylation levels are higher in 4-m shoots than in 2-m shoots. We also detected shorter poly(A) tail lengths (PALs) in 4-m shoots compared with 2-m shoots. Genes showing differential PAL were mainly enriched in the functional terms of protein translation and vesicle fusion. An association analysis between PALs and DNA methylation strongly suggested that gene body CG methylation levels are positively associated with PAL. This study provides valuable information to better understand post-transcriptional regulations responsible for fast-growing shoots in Moso bamboo.
Machine learning identifies a profile of inadequate responder to methotrexate in rheumatoid arthritis
Authors: Duquesne Julien , Bouget Vincent , Cournède Paul Henry , Fautrel Bruno , Guillemin Francis , de Jong Pascal H P , Heutz Judith W , Verstappen Marloes , van der Helm-van Mil Annette H M , Mariette Xavier , Bitoun Samuel 
Published: November 2022

AbstractObjectivesAround 30% of patients with RA have an inadequate response to MTX. We aimed to use routine clinical and biological data to build machine learning models predicting EULAR inadequate response to MTX and to identify simple predictive biomarkers.MethodsModels were trained on RA patients fulfilling the 2010 ACR/EULAR criteria from the ESPOIR and Leiden EAC cohorts to predict the EULAR response at 9 months (± 6 months). Several models were compared on the training set using the AUROC. The best model was evaluated on an external validation cohort (tREACH). The model's predictions were explained using Shapley values to extract a biomarker of inadequate response.ResultsWe included 493 therapeutic sequences from ESPOIR, 239 from EAC and 138 from tREACH. The model selected DAS28, Lymphocytes, Creatininemia, Leucocytes, AST, ALT, swollen joint count and corticosteroid co-treatment as predictors. The model reached an AUROC of 0.72 [95% CI (0.63, 0.80)] on the external validation set, where 70% of patients were responders to MTX. Patients predicted as inadequate responders had only 38% [95% CI (20%, 58%)] chance to respond and using the algorithm to decide to initiate MTX would decrease inadequate-response rate from 30% to 23% [95% CI: (17%, 29%)]. A biomarker was identified in patients with moderate or high activity (DAS28 &gt; 3.2): patients with a lymphocyte count superior to 2000 cells/mm3 are significantly less likely to respond.ConclusionOur study highlights the usefulness of machine learning in unveiling subgroups of inadequate responders to MTX to guide new therapeutic strategies. Further work is needed to validate this approach.
Sleep efficiency and the metabolic risk score in very active older women and men
Authors: Madden Kenneth M , Feldman Boris , Chase Jocelyn 
Published: November 2022

AbstractStudy ObjectivesSleep disruption is a risk factor for obesity, diabetes, and cardiovascular disease in older adults. How physical activity (PA) interacts with the negative cardiometabolic effects of poor sleep is not known. We objectively measured sleep efficiency (SE) in very active older adults and examined the association between SE and a continuous Metabolic Syndrome Risk Score (cMSy).MethodsVery active older adults (age ≥65 years) from a Master’s Ski Team (Whistler, Canada) were recruited. Each participants wore an activity monitor (SenseWear Pro) continuously for 7 days to provide measures of both daily energy expenditure (metabolic equivalents, METs) and SE. All components of the metabolic syndrome were measured and a principal component analysis was used to compute a continuous metabolic risk score (cMSy, sum of eigenvalues ≥1.0).ResultsA total of 54 participants (mean age 71.4 years, SD 4.4 years, and 24 men and 30 women) were recruited and had very high PA levels (&gt;2.5 h per day of exercise). Initially, there was no significant association between SE and cMSy (p = 0.222). When stratified by biological sex, only men showed a significant negative association between SE and cMSy (Standardized β = −0.364 ± 0.159, p = 0.032).ConclusionsOnly older men show a significant negative association between poor SE and increased cardiometabolic risk, despite high levels of PA.
Guardian Trust revisited
Authors: de Lacey Joseph , Herrett Niamh 
Published: November 2022

Abstract
When a third party threatens a claim in relation to trust assets, and the time for distribution has arisen, the trustee is placed in a difficult position. To distribute notwithstanding the threatened claim could result in personal liability for the trustee under the Guardian Trust principle. To not distribute, whilst the threatened claim is outstanding, could lead to the paralysis of the trust for months, if not years. This article considers the availability of ‘put up or shut up’ orders against the threatening party in such circumstances. What is the jurisdiction to make such an order, what are its requirements, and might a trustee be justified in utilising ‘put up or shut up’ orders more often and more quickly?
Responding to the cuts in UK AID to neglected tropical diseases control programmes in Africa
Authors: Anderson Roy M , Cano Jorge , Hollingsworth T Déirdre , Deribe-Kassaye Kebede , Zouré Honorat G M , Kello Amir B , Impouma Benido , Kalu Akpaka A , Appleby Laura , Yard Elodie , Salasibew Mihretab , McRae-McKee Kevin , Vegvari Carolin 
Published: November 2022

AbstractThe early termination of the Accelerating the Sustainable Control and Elimination of Neglected Tropical Diseases (Ascend) programme by the UK government in June 2021 was a bitter blow to countries in East and West Africa where no alternative source of funding existed. Here we assess the potential impact the cuts may have had if alternative funding had not been made available by new development partners and outline new strategies developed by affected countries to mitigate current and future disruptions to neglected tropical disease control programmes.
Piezoelectric Osteotomy versus Conventional Osteotomy in Rhinoplasty: A Systematic Review and Meta-analysis
Authors: Khajuria Ankur , Krzak Ada M. , Reddy Rohin K , Lai Kenneth , Wignakumar Thirushan , Rohrich Rod J. 
Published: November 2022

Introduction:
Previous systematic reviews evaluating piezoelectric osteotomy are of critically low quality. We conducted a high-quality systematic review and meta-analysis to evaluate outcomes for piezoelectric versus conventional osteotomy.

Methods:
The study protocol was published a priori (PROSPERO: CRD42021287877). MEDLINE, Embase, Web of Science, and CENTRAL were searched for studies comparing piezoelectric versus conventional osteotomes and reporting at least one outcome of interest (clinical or patient-reported outcomes, PROs). Methodological quality and risk of bias were assessed using GRADE and Cochrane’s RoB-2/ROBINS-I tools, respectively. Random effects models were applied.

Results:
Of 347 articles, 10 studies (nine randomized controlled trials; one prospective cohort study) including 554 patients were included. Piezoelectric osteotomy was associated with significantly reduced edema [standardized mean difference (SMD), −0.67; 95% confidence interval (CI), −1.03 to −0.30; P < 0.0004], ecchymosis (SMD, −0.93; 95% CI, −1.13 to −0.73; P < 0.00001), and pain (SMD, −1.48; 95% CI, −2.07 to −0.88; P < 0.00001) compared with standard osteotomy. Odds of mucosal injury were significantly lower following piezoelectric osteotomy (odds ratio, 0.06; 95% CI, 0.01 to 0.52; P = 0.01). There was no difference in duration of osteotomy (SMD, 3.15; 95% CI, −1.82 to 8.12; P = 0.22) or total procedure duration (SMD, 0.46; 95% CI, −0.43 to 1.36; P = 0.31). One study reported PROs, favoring piezoelectric osteotomy.

Conclusion:
This systematic review and meta-analysis provides support (albeit weak, due to low-quality evidence) for piezoelectric over conventional osteotomy, for reducing morbidity in the early postoperative period. High-quality level I data reporting PROs will optimize shared decision-making/informed consent.
Abdominal Wall Reconstruction in Adults With Exstrophy of the Bladder
Authors: Ete Geley , Cordelia MJ Felix , Kingsly Paul M. , Akamanchi Anirudha K. , Agarwal Shwetha 
Published: November 2022

Introduction
Abdominal wall reconstruction in an adult patient with exstrophy bladder is challenging. A variety of local and regional flaps are described. We describe our experience with a 3-layer technique with the differential reconstruction of the fascial and cutaneous layer.

Patient and Methods
Three adult patients with untreated bladder exstrophy were included in the study period from 2017 and 2019. The surgical technique involved 3-layer abdominal reconstruction involving closure with unilateral anterior rectus sheath turnover and a pedicled anterolateral thigh flap for skin cover reinforced with a mesh between the two.

Results
All three were male patients with an average age of 22.3 years. The average size of the defect was 10 × 9 cm. The mean period of follow-up was 6 months (range, 2–18 months). In all 3 patients, the flaps settled well with no complications.

Conclusions
Although rare as they may be, the management of untreated bladder exstrophy presenting in adulthood has evolved over the years. The goals of the management have changed from simple defect closure to the dynamic reconstruction of the abdominal wall covering a continent neobladder. Our technique of a 3-layer closure can provide good functional integrity to the abdominal wall even in large defects.
Functional Thenar Reconstruction
Authors: Tadisina Kashyap K. , Kareh Aurora M. , Hasan Samir , Frojo Gianfranco , Xu Kyle Y. 
Published: November 2022

Abstract
Reconstruction of the thumb is among the most complex challenges faced by hand surgeons. Meaningful functional recovery of the thumb is dependent mainly on thumb opposition and palmar abduction. Free functional muscle transfer provides neurotized, robust soft tissue coverage that can achieve dynamic reconstruction of thenar musculature in a single stage.
We present a case of a free neurotized segmental gracilis muscle transfer for thenar reconstruction and a systematic review of thenar reconstruction with free functional muscle transfer in the literature. A teenage male patient with a gunshot-induced thenar defect was reconstructed using a free neurotized gracilis muscle measuring 5 × 11 cm. The obturator nerve was coapted to the recurrent motor branch of the median nerve. The patient reached M4 strength at 10 months with functional use of his thumb. A systematic review of options for functional thenar reconstruction revealed 14 studies describing functional thenar reconstruction in 44 patients. Successful functional flaps described included gracilis muscle, pronator quadratus muscle, pectoralis minor muscle, abductor hallucis muscle, extensor digitorum brevis muscle, and serratus anterior muscle. Microsurgical transfer of a functional muscle is an excellent option for single-stage thenar reconstruction of both form and function. There are a number of available donor sites with equivalent size and bulk to that of native thenar musculature.
The Impact of Oncoplastic Reduction on Initiation of Adjuvant Radiation and Need for Reexcision
Authors: Shah Jennifer K. , Lipman Kelsey , Pedreira Rachel , Makarewicz Nathan , Nazerali Rahim 
Published: November 2022

Introduction
Partial breast reconstruction with oncoplastic reduction can provide breast cancer patients with improved aesthetic outcomes after breast conservation therapy. This study evaluates the implications of simultaneous oncoplastic reduction with lumpectomy on complication rates, time to adjuvant radiation therapy, and rates of margin reexcision compared with lumpectomy alone.

Methods
The Clinformatics Data Mart Database is a national deidentified commercial claims data warehouse. From 2003 to 2020, adult female patients were queried to identify patients with a breast cancer diagnosis with International Classification of Disease codes. Among those, current procedural terminology codes were used to identify those who underwent lumpectomy alone versus lumpectomy with oncoplastic reduction. Patient demographics, complications, adjuvant oncologic therapies, and need for reexcision were recorded. Patients not continuously enrolled for at least 6 months before and after the index procedure were excluded. Multivariable regression and χ2 tests were used for statistical analysis.

Results
Of 53,165 patients meeting criteria (mean age, 61.4 ± 11.6 years), 1552 (2.9%) underwent oncoplastic reduction. Diagnoses of most nonsurgical complications (seroma, wound dehiscence, postoperative infection, fat necrosis, tissue necrosis, and nonspecified complications of surgical care) were significantly higher in the oncoplastic reduction group, as were rates of some surgical complications (hematoma, seroma, and tissue debridement). However, undergoing oncoplastic reduction did not impact time to adjuvant radiation (P = 0.194) and protected against positive margins requiring repeat lumpectomy or completion mastectomy (P < 0.001).

Conclusions
In patients undergoing breast conservation therapy, simultaneous oncoplastic reduction decreased occurrence of positive margins and did not impact time to adjuvant radiation therapy despite increased rates of surgical and nonsurgical complications.
Lesion Site Is the Key Prognostic Factor for Keloid Patients Receiving Surgery With Adjuvant Radiotherapy
Authors: Chen Frank , Kuo Yur-Ren , Huang Chih-Jen , Tang Jen-Yang , Chiang Chen-Han , Huang Ming-Yii 
Published: November 2022

Background
Keloid is a benign tumor with high recurrence rate; accordingly, complete surgical excision with adjuvant radiotherapy is one of the most effective treatments. This study reviewed outcomes of keloid patients receiving surgery and adjuvant radiotherapy in Kaohsiung Medical University Hospital.

Materials and Methods
All patients received radiation dose with 15 Gy, with their first radiotherapy within 24 hours after surgical excision. The end points were recurrence rate and local recurrence-free interval (LRFI), defined clinically as palpable gross tumor over the treatment site and duration from the last day of radiotherapy to disease recurrence.

Results
From May 2017 to July 2020, 32 patients with 40 keloid lesions were included. The mean age for these patients was 37.6 years, and the median follow-up time was 15.3 months. The overall recurrence rate was 52.5%, and the median LRFI was 9.7 months. Recurrence rates for males and females were 46.7% and 56% (P = 0.567), respectively; for head and ear, chest, shoulder and upper extremities, and abdomen and back were 12.5%, 61.5%, 63.6%, and 62.5% (P = 0.093); for lesions over 20 cm2 and below 20 cm2 were 62.5% and 50% (P = 0.527); and for megavoltage electron beam and kilovoltage photon beam were 56.7% and 40% (P = 0.361), respectively. Patients were further classified into 2 groups by lesion sites, which showed lower recurrence rate (P = 0.011) and longer LRFI (P = 0.028) with lesions over the head and ear than other sites.

Conclusions
We found that lesion site might be a prognostic factor for keloid recurrence. Adjuvant radiation dose escalation for high-recurrence risk areas (other than the head and ear) might be required.
Outcomes Analysis of Textured Versus Smooth Tissue Expanders in Breast Reconstruction
Authors: Di Valerio Elizabeth , Rao Aditya Narayan , Leyngold Mark , Carlson Jacob , O'Neill Daniel , Virk Sarah , Mast Bruce , Satteson Ellen 
Published: November 2022

Introduction
Because of concerns related to the correlation of breast implant–associated anaplastic large cell lymphoma (BIA-ALCL) and textured implants, the use of smooth devices in breast reconstruction has been increasing. Currently, there is a paucity of literature evaluating the safety of smooth tissue expanders (STEs), which are now being used more frequently in first-stage breast reconstruction. This study sought to compare the safety and outcomes associated with STEs compared with textured tissue expanders in prosthesis-based breast reconstruction.

Methods
A single-institution retrospective review of 394 patients undergoing tissue expander-based breast reconstruction (147 smooth and 247 textured) between 2015 and 2019 was conducted. Patient demographics, comorbidities, treatment characteristics, complications, and surgical outcomes were evaluated. Data analysis was performed using Fisher exact and t tests.

Results
No significant difference in demographics or complication rates were identified, including rates of hematoma, seroma, wound dehiscence, delayed wound healing, infection, tissue expander malposition, nipple necrosis, mastectomy flap necrosis, reoperation, readmission, and explantation. Average follow-up was 19 and 22 months for the smooth and textured groups, respectively. No cases of BIA-ALCL were identified in either group.

Conclusions
With equivocal safety profiles and no demonstrated risk in BIA-ALCL associated with STEs, this study supports the safety of using STEs compared with textured tissue expanders in prosthesis-based breast reconstruction with the advantage in preventing BIA-ALCL and concludes that there is no role for textured breast expanders.