bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting hepatocellular carcinoma early recurrence after ablation based on magnetic resonance imaging radiomics nomogram
Authors: Yang Xiaozhen , Yuan Chunwang , Zhang Yinghua , Li Kang , Wang Zhenchang 
Published: December 2022

Background:
The aim of this study is to investigate a model for predicting the early recurrence of hepatocellular carcinoma (HCC) after ablation.

Methods:
A total of 181 patients with HCC after ablation (train group was 119 cases; validation group was 62 cases) were enrolled. The cases of early recurrence in the set of train and validation were 63 and 31, respectively. Radiomics features were extracted from the enhanced magnetic resonance imaging scanning, including pre-contrast injection, arterial phase, late arterial phase, portal venous phase, and delayed phase. The least absolute shrinkage and selection operator cox proportional hazards regression after univariate and multivariate analysis was used to screen radiomics features and build integrated models. The nomograms predicting recurrence and survival of patients of HCC after ablation were established based on the clinical, imaging, and radiomics features. The area under the curve (AUC) of the receiver operating characteristic curve and C-index for the train and validation group was used to evaluate model efficacy.

Results:
Four radiomics features were selected out of 34 texture features to formulate the rad-score. Multivariate analyses suggested that the rad-score, number of lesions, integrity of the capsule, pathological type, and alpha-fetoprotein were independent influencing factors. The AUC of predicting early recurrence at 1, 2, and 3 years in the train group was 0.79 (95% CI: 0.72–0.88), 0.72 (95% CI: 0.63–0.82), and 0.71 (95% CI: 0.61–0.83), respectively. The AUC of predicting early recurrence at 1, 2, and 3 years in the validation group was 0.72 (95% CI: 0.58–0.84), 0.61 (95% CI: 0.45–0.78) and 0.64 (95% CI: 0.40–0.87).

Conclusion:
The model for early recurrence of HCC after ablation based on the clinical, imaging, and radiomics features presented good predictive performance. This may facilitate the early treatment of patients.
Exploration of the Relationships Between Stress and Distinct Pain and Sleep Disturbance Profiles in Patients Undergoing Chemotherapy
Authors: Romanovska Vita , Block Astrid , Paul Steven M. , Cooper Bruce A. , Hammer Marilyn J. , Conley Yvette P. , Levine Jon D. , Kober Kord M. , Miaskowski Christine 
Published: December 2022

Background
Unrelieved pain and sleep disturbance are common symptoms in oncology patients. Increased stress may be an underlying cause for both symptoms.

Objectives
The purposes of this study were to identify subgroups of outpatients with distinct pain and sleep disturbance profiles and to evaluate differences among these subgroups in demographic and clinical characteristics. Differences in global stress, cancer-specific stress, and cumulative life stress, as well as resilience and coping, were evaluated.

Methods
Patients (N = 1343) completed self-report questionnaires for demographic and clinical characteristics and stress, resilience, and coping. Latent profile analysis was used to identify subgroups of patients with distinct pain and sleep disturbance profiles. Differences among the subgroups were determined using parametric and nonparametric tests.

Results
Three distinct profiles were identified (ie, No Pain + Moderate Sleep Disturbance (SD) (27.6%), Moderate Pain + Moderate SD (38.6%), Severe Pain + High SD (33.8%)). Compared with the other 2 classes, Severe Pain + High SD class was younger, had fewer years of education, was more likely to be female, more likely to live alone, less likely to be employed, and had a higher level of comorbidity. This class had the highest stress scores and was more likely to report higher rates of adverse childhood experiences.

Conclusion
Over 70% of our sample reported clinically meaningful levels of both symptoms, and 33.8% reported relatively high rates of adverse childhood experiences.

Implication for Practice
Clinicians need to perform routine assessments, particularly of adverse childhood experiences, and initiate appropriate referrals.
Findings From a Scoping Review: Presumptive Treatment for Chlamydia trachomatis and Neisseria gonorrhoeae in the United States, 2006–2021
Authors: Allen Katie S. , Hinrichs Rachel , Heumann Christine L. , Titus Melissa K. , Duszynski Thomas J. , Valvi Nimish R. , Wiensch Ashley , Tao Guoyu , Dixon Brian E. 
Published: December 2022

Abstract

Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) are the 2 most common reported sexually transmitted infections in the United States. Current recommendations are to presumptively treat CT and/or GC in persons with symptoms or known contact. This review characterizes the literature around studies with presumptive treatment, including identifying rates of presumptive treatment and overtreatment and undertreatment rates. Of the 18 articles that met our inclusion criteria, 6 pertained to outpatient settings. In the outpatient setting, presumptive treatment rates, for both asymptomatic and symptomic patients, varied from 12% to 100%, and the percent positive of those presumptively treated ranged from 25% to 46%. Three studies also reported data on positive results in patients not presumptively treated, which ranged from 2% to 9%. Two studies reported median follow-up time for untreated, which was roughly 9 days. The remaining 12 articles pertained to the emergency setting where presumptive treatment rates, for both asymptomatic and symptomic patients, varied from 16% to 91%, the percent positive following presumptive treatment ranged from 14% to 59%. Positive results without presumptive treatment ranged from 4% to 52%. Two studies reported the percent positive without any treatment (6% and 32%, respectively) and one reported follow-up time for untreated infections (median, 4.8 days). Rates of presumptive treatment, as well as rates of overtreatment or undertreatment vary widely across studies and within care settings. Given the large variability in presumptive treatment, the focus on urban settings, and minimal focus on social determinants of health, additional studies are needed to guide treatment practices for CT and GC in outpatient and emergency settings.
Three-Dimensional Quantitative Assessment of Condylar Displacement and Adaptive Remodeling in Asymmetrical Mandibular Prognathism Patients After Sagittal Split Ramus Osteotomy
Authors: Jha Nayansi , Kim MyungSu , Cevidanes Lucia , Kim Yoon-Ji 
Published: December 2022

This study was performed to evaluate the condylar displacement and associated condylar remodeling in class III patients following mandibular setback surgery via sagittal split ramus osteotomy (SSRO). The sample comprised of 26 condyles of 13 subjects (mean age of 21.2±2.6 y). We evaluated patients with mandibular prognathism and facial asymmetry who had undergone SSRO for mandibular setback at Korea University Hospital between January 2016 and December 2018. Three-dimensional segmentation of the mandibular condyles was done using the initial cone-beam computed tomography scan and scan taken 12 months postoperatively or later. Quantitative assessments of the 3-dimensional condylar displacement from T0 to T1 and bony remodeling of 8 regions of the condylar head were performed. The correlation between the condylar displacement and condylar head remodeling on the deviated (D) and nondeviated (ND) sides was analyzed. Significant correlations between condylar displacement and surface remodeling were observed in both D and ND condyles. The anteroposterior condylar displacement was significantly different between the D and ND sides (P=0.007). There was no significant difference in condylar remodeling between the 2 sides. Condylar displacement and adaptive remodeling after SSRO varied greatly among individuals. Compared with displacement in the ND condyle, displacement in the D condyle has a greater association with condylar remodeling in both D and ND condyles. There is no significant difference in condylar head remodeling between D and ND condyles.
Trends in Craniofacial Fellowship Career Outcomes: A Call for Expanding Professional Opportunities in Craniofacial Surgery
Authors: Rogers Ashley E. , Sayyed Adaah A. , Marable Julian , Harshbarger Raymond , Taub Peter J. , Taylor Jesse , Baker Stephen B. 
Published: December 2022

Purpose:
Limited available pediatric plastic surgery positions fail to accommodate the increasing number of craniofacial fellows trained annually. However, many adult indications have increased the demand for craniofacial expertise. Given new opportunities available to craniofacial surgeons, the authors aim to evaluate career prospects for recent craniofacial graduates and explore additional career opportunities.

Methods:
Upon approval from the American Society of Craniofacial Surgeons (ASCFS), an anonymous online survey invitation was sent to craniofacial fellows who graduated from 2016 to 2021. Respondents were queried regarding their craniofacial fellowship and subsequent career prospects.

Results:
A total of 124 eligible participants were identified, of which 30 (24.2%) responded. Craniomaxillofacial case distribution at respondents’ current practices varied, with 42.3% reporting a 50% to 75% craniofacial caseload and 38.5% reporting less than 25%. Craniofacial trauma reconstruction was performed most at current positions (92.3%), followed by general reconstruction (92.3%) and breast surgery (69.2%); the least commonly performed was facial feminization (23.1%). Most respondents desired an increased craniomaxillofacial caseload (65.4%). However, 26.9% were unable to secure their current position before fellowship completion, and 80.0% cited limited craniofacial job availability. Recommendations to improve fellowship comprehensiveness and increase candidate competitiveness included increased facial feminization, facial esthetic, and microsurgical experience.

Conclusion:
To adapt to trends in craniomaxillofacial surgery, ASCFS should encourage developing fellowships that increase exposure to gender-affirming, adult craniofacial reconstruction, orthognathic, and skeletal facial esthetic surgery. Expanding training beyond congenital deformities can provide additional employment opportunities while maintaining excellence and innovation in facial plastic surgery.
Malrotation and Fibroblast Growth Factor Receptor-2–Associated Craniosynostosis: An Underrecognized Association and Management Pathway
Authors: Harwood Rachel , O’Shea Kathryn , Hennedige Anusha , Parks Christopher , Turnock Colette , Wood Sarah 
Published: December 2022

Introduction:
Feeding difficulties are common and multifactorial in children with Fibroblast Growth Factor Receptor-2 (FGFR-2) mutations. Intestinal rotation anomalies have been demonstrated to occur more frequently in animals with FGFR-2 mutations. This study aims to describe intestinal rotation anomalies, surgical management, and feeding assistance in children with FGFR-2 mutations who have undergone upper gastrointestinal (UGI) contrast studies.

Methods:
Retrospective data were collected of children born between 1988 and 2020 in a UK quaternary craniofacial unit with FGFR-2–associated craniosynostosis. A consultant survey of approach to malrotation was undertaken.

Results:
Thirty-four children were included, 17 (50%) female. Six (18%) had UGI symptoms, which included bilious vomiting (n=2), nonbilious vomiting (n=5), retching (n=1), feed intolerance (n=3), and failure to thrive (n=3). Nine had a gastrostomy in situ. Intestinal rotation anomalies occurred in 4 (12%) children, 3 of whom underwent a Ladd procedure and two third required gastrojejunal feeding postoperatively. Consultants agreed that all children with FGFR-2 mutation and UGI symptoms should undergo UGI contrast study, as should children requiring a gastrostomy.

Discussion:
Intestinal rotation anomalies in children with FGFR-2 mutations occur more frequently than the general population. Prompt consideration of UGI contrast in symptomatic children with FGFR-2 mutation is recommended to enable early surgical management of children with malrotation.
Spontaneous Closure of Congenital Cranial Defect: Is Early Surgical Intervention Warranted?
Authors: Seu Michelle Y. , Aminzada Amir , Harmon Kelly A. , Guidetti Martina , Espinoza Orías Alejandro A. , Figueroa Alvaro A. , Tragos Christina 
Published: December 2022

Infantile cranial development typically occurs in a predictable sequence of events; however, less is known about how the development occurs in isolated, nonsyndromic congenital craniofacial anomalies. Furthermore, the timing of pediatric cranioplasty has been extrapolated from adult studies. Thus, the management of nonsyndromic congenital craniofacial anomalies presents with unique challenges to the craniofacial surgeon. The authors describe the case of a baby girl who was born with right Tessier 3 cleft, cleft palate, anophthalmos, and severe left craniofacial microsomia with Pruzansky grade III left mandibular anomaly. By analyzing 3-dimensional chronological models of the patient, the authors found that her abnormal fontanelle initially increased in size until 22 weeks of age, with subsequent spontaneous closure at a rate of 60.53 mm2/y. Although similar cranial anomalies are typically surgically corrected early in life, delaying treatment until after 2 years of age may be appropriate in some patients, obviating surgical morbidity in the newborn period.
Amplified Natural Killer Cell Activity and Attenuated Regulatory T-cell Function Are Determinants for Corneal Alloimmunity in Very Young Mice
Authors: Nakao Takeshi , Inomata Takenori , Blanco Tomas , Musayeva Aytan , Tahvildari Maryam , Amouzegar Afsaneh , Yin Jia , Chauhan Sunil K. , Chen Yihe , Dana Reza 
Published: December 2022

Background.
Corneal transplantation outcomes are generally less favorable in young children compared with adults. The purpose of this study was to determine the immunological mechanisms underlying this difference.

Methods.
A murine model of allogeneic corneal transplantation was used in the study, and graft survival was determined by evaluating opacity scores for 8 wk. Syngeneic transplantation in the very young host served as a surgical control. The frequencies of total and activated natural killer (NK) cells in cornea posttransplantation were kinetically evaluated using flow cytometry. The regulatory T cell (Treg) frequency and function in naive animals were assessed by flow cytometry and in vitro suppression assays, respectively. Finally, graft survival and immune responses were determined in NK cell–depleted, or adult naive Treg-transferred, young hosts.

Results.
Corneal allograft survival in the very young recipients was significantly lower than in adult hosts. The frequencies of total NK cells and their interferon gamma–expressing subset in the cornea were significantly higher in the very young mice posttransplantation. In ungrafted mice, frequencies of Treg in draining lymph nodes as well as their capabilities to suppress NK-cell secretion of interferon gamma were lower in the very young compared with adults. In NK cell–depleted or adult Treg–-transferred very young recipients, the allograft survival was significantly improved along with the suppressed NK-cell response.

Conclusions.
Our data demonstrate that amplified activity of NK cells, together with lower suppressive function of Treg, contributes to early rejection of corneal allografts in very young graft recipients.
Process Optimization of Plasma Bubbling Set Up for Cow Milk Decontamination and Quality Evaluation
Authors: Dash Samarpita , Jaganmohan Rangarajan 
Published: December 2022

AbstractCold plasma aims to decontaminate and maintain the naturality of the food. The present study discussed the application of novel plasma bubbling for raw milk pasteurization with different combinations of processing parameters such as voltage, flow rate of air, time interval and volume. The observation showed a decline in microbial load, with an increase in pH value up to 6.9 at optimised conditions (200 volts, the flow rate of air 10 Litres/hour, time 15 minutes and volume 100 mL). The optimized condition was observed was found to be appropriate and could be beneficial to the food industry.
One-shot design elevates functional expression levels of a voltage-gated potassium channel
Authors: Weinstein Jonathan Jacob , Saikia Chandamita , Karbat Izhar , Goldenzweig Adi , Reuveny Eitan , Fleishman Sarel Jacob 
Published: December 2022

AbstractMembrane proteins play critical physiological roles as receptors, channels, pumps, and transporters. Despite their importance, however, low expression levels often hamper the experimental characterization of membrane proteins. We present an automated and web-accessible design algorithm called mPROSS (https://mPROSS.weizmann.ac.il), which uses phylogenetic analysis and an atomistic potential, including an empirical lipophilicity scale, to improve native-state energy. As a stringent test, we apply mPROSS to the Kv1.2-Kv2.1 paddle chimera voltage-gated potassium channel. Four designs, encoding 9-26 mutations relative to the parental channel, were functional and maintained potassium-selective permeation and voltage dependence inXenopusoocytes with up to 14-fold increase in whole-cell current densities. Additionally, single-channel recordings reveal no significant change in the channel-opening probability nor in unitary conductance, indicating that functional expression levels increase without impacting the activity profile of individual channels. Our results suggest that the expression levels of other dynamical channels and receptors may be enhanced through one-shot design calculations.Significance statementHeterologous expression levels of membrane proteins are often low, limiting research and applications. We combine homologous-sequence analysis with Rosetta atomistic calculations to enable one-shot design of dozens of mutations that improve native-state energy. Applied to a voltage-gated potassium channel, designs exhibited up to 14-fold improved functional expression levels in oocytes with almost no change in the single-channel activity profile. This design approach may accelerate research of many challenging membrane proteins, including receptors, channels, and transporters.
High-quality nuclear genome and mitogenome ofBipolaris sorokinianastrain LK93, a devastating pathogen causing wheat root rot
Authors: Zhang Wanying , Yang Qun , Yang Lei , Li Haiyang , Zhou Wenqing , Meng Jiaxing , Hu Yanfeng , Wang Limin , Kang Ruijiao , Li Honglian , Ding Shengli , Li Guotian 
Published: December 2022

AbstractBipolaris sorokiniana, one of the most devastating hemibiotrophic fungal pathogens, causes root rot, crown rot, leaf blotching, and black embryos of gramineous crops worldwide, posing a serious threat to global food security. However, the host-pathogen interaction mechanism betweenB. sorokinianaand wheat remains poorly understood. To facilitate related studies, we sequenced and assembled the genome ofB. sorokinianastrain LK93. Nanopore long reads and next generation sequencing short reads were applied in the genome assembly, and the final 36.4 Mb genome assembly contains 16 contigs with the contig N50 of 2.3 Mb. Subsequently, we annotated 11,811 protein-coding genes including 10,620 functional genes, 258 of which were identified as secretory proteins including 211 predicted effectors. Additionally, the 111,581 bp mitogenome of LK93 was assembled and annotated. The LK93 genomes presented in this study will facilitate research in theB. sorokiniana-wheat pathosystem for better control of crop diseases.
Species boundaries to the limit: validating species delimitation methods is critical to avoid taxonomic inflation in the genomic era
Authors: Burriel-Carranza Bernat , Estarellas Maria , Riaño Gabriel , Talavera Adrián , Tejero-Cicuéndez Héctor , Els Johannes , Carranza Salvador 
Published: December 2022

AbstractWith the advent of molecular phylogenetics, the number of taxonomic studies unveiling and describing cryptic diversity has greatly increased. However, speciation between cryptic lineages is often defined without evaluating population structure or gene flow, which can lead to false claims of species status and, subsequently, taxonomic inflation. In the present study we focus on the intriguing case of the Arabian geckoTrachydactylus hajarensis(Squamata: Gekkonidae), a species for which cryptic diversity has been previously reported. We generated mitochondrial data (12S rDNA) and genome-wide SNP data (ddRADseq) for 52 specimens to determine phylogenomic relationships, population structure and gene flow within this species. Then, we applied species delimitation methods (SDMs) to evaluate several competing species hypotheses through the Multispecies Coalescent model. Results show thatT. hajarensisis comprised by three well-defined lineages, two of them in the Hajar Mountains of eastern Arabia, and one in Masirah Island, in the southeastern coast of Oman. Even though high levels of past introgression and strong mitonuclear discordances were found, current gene flow is scarce with clear boundaries between populations and shallow levels of admixture in the contact zone between lineages. Surprisingly, species tree topology differed between methods and when different individuals were used in downsampled datasets. Conventional SDMs supported up to three putative new species within the group. However, after species validation with the genealogical divergence index (gdi), none of the putative species held. Overall, this study highlights the importance of sample choice, integrative analyses, and validation methods to not incur into taxonomic inflation, providing a set of already available tools to assess and validate population structure, gene flow, and SDMs before describing new species.
Nicotiana benthamiana XYLEM CYSTEINE PROTEASEgenes facilitate tracheary element formation in interfamily grafting
Authors: Huang Chaokun , Kurotani Ken-ichi , Tabata Ryo , Mitsuda Nobutaka , Sugita Ryohei , Tanoi Keitaro , Notaguchi Michitaka 
Published: December 2022

AbstractGrafting is a plant propagation technique widely used in agriculture. A recent discovery of the capability of interfamily grafting inNicotianahas expanded the potential combinations of grafting. In this study, we showed that xylem connection is essential for the achievement of interfamily grafting and investigated the molecular basis of xylem formation at the graft junction. Transcriptome and gene network analyses revealed gene modules for tracheary element (TE) formation during grafting that include genes associated with xylem cell differentiation and immune response. The reliability of the drawn network was validated by examining the role of theNicotiana benthamiana XYLEM CYSTEINE PROTEASE (NbXCP)genes in TE formation during interfamily grafting. Promoter activities ofNbXCP1andNbXCP2genes were found in differentiating TE cells in the stem and callus tissues at the graft junction. Analysis of aNbxcp1;Nbxcp2loss-of-function mutant indicated thatNbXCPscontrol the timing ofde novoTE formation at the graft junction. Moreover, grafts of theNbXCP1overexpressor increased the scion growth rate as well as the fruit size. Thus, we identified gene modules for TE formation at the graft boundary and demonstrated potential ways to enhanceNicotianainterfamily grafting.