bluuebunny/crossref_metadata_2025 huggingface dataset:
IGF signaling pathway in bone and cartilage development, homeostasis, and disease
Authors: Ruan Xinyi , Jin Xiuhui , Sun Fuju , Pi Jiashun , Jinghu Yihan , Lin Xinyi , Zhang Nenghua , Chen Guiqian
Published: August 2024

The skeleton plays a fundamental role in the maintenance of organ function and daily activities. The insulin‐like growth factor (IGF) family is a group of polypeptide substances with a pronounced role in osteoblast differentiation, bone development, and metabolism. Disturbance of the IGFs and the IGF signaling pathway is inextricably linked with assorted developmental defects, growth irregularities, and jeopardized skeletal structure. Recent findings have illustrated the significance of the action of the IGF signaling pathway via growth factors and receptors and its interactions with dissimilar signaling pathways (Wnt/β‐catenin, BMP, TGF‐β, and Hh/PTH signaling pathways) in promoting the growth, survival, and differentiation of osteoblasts. IGF signaling also exhibits profound influences on cartilage and bone development and skeletal homeostasis via versatile cell–cell interactions in an autocrine, paracrine, and endocrine manner systemically and locally. Our review summarizes the role and regulatory function as well as a potentially integrated gene network of the IGF signaling pathway with other signaling pathways in bone and cartilage development and skeletal homeostasis, which in turn provides an enlightening insight into visualizing bright molecular targets to be eligible for designing effective drugs to handle bone diseases and maladies, such as osteoporosis, osteoarthritis, and dwarfism.
Anterior Column Release
Authors: Pressman Elliot , Monsour Molly , Goldman Hannah , Kumar Jay I. , Noureldine Mohammad Hassan A. , Alikhani Puya
Published: August 2024

Study Design:

Retrospective review.

Objective:

We sought to characterize complications associated with anterior column release (ACR).

Summary of Background Data:

Correction of positive sagittal imbalance was traditionally completed with anterior column grafts or posterior osteotomies. ACR is a minimally invasive technique for addressing sagittal plane deformity by restoring lumbar lordosis.

Methods:

We conducted a retrospective review of consecutive patients who underwent ACR in a prospectively kept database at a tertiary care academic center from January 2012 to December 2018. The prespecified complications were hardware failure (rod fracture, hardware loosening, or screw fracture), proximal junctional kyphosis, ipsilateral thigh numbness, ipsilateral femoral nerve weakness, arterial injury requiring blood transfusion, bowel injury, and abdominal pseudohernia.

Results:

Thirty-eight patients were identified. Thirty-five patients had ACR at L3-4, 1 had ACR at L4-5, and 1 patient had ACR at L2-3 and L3-4. Eighteen patients (47.4%) had one of the prespecified complications (10 patients had multiple). Ten patients developed hardware failure (26.3%); 8 patients (21.1%) had rod fracture, 4 (10.5%) had screw fracture, and 1 (2.6%) had screw loosening. At discharge, rates of ipsilateral thigh numbness (37.8%) and hip flexor (37.8%)/quadriceps weakness (29.7%) were the highest. At follow-up, 6 patients (16.2%) had ipsilateral anterolateral thigh numbness, 5 (13.5%) suffered from ipsilateral hip flexion weakness, and 3 patients (5.4%) from ipsilateral quadriceps weakness. Arterial injury occurred in 1 patient (2.7%). Abdominal pseudohernia occurred in 1 patient (2.7%). There were no bowel injuries observed.

Conclusions:

ACR is associated with a higher than initially anticipated risk of neurological complications, hardware failure, and proximal junctional kyphosis.
Brief Communication: Treatment Outcomes for Advanced Melanoma of Unknown Primary Compared With Melanoma With Known Primary
Authors: Persa Oana-Diana , Hassel Jessical Cecile , Steeb Theresa , Erdmann Michael , Karimi Bita , Stege Henner , Klespe Kai Christian , Schatton Kerstin , Tomsitz Dirk , Rübben Albert , Thiem Alexander , Berking Carola , Biedermann Tilo
Published: August 2024

Most patients with advanced melanomas have a known primary site [melanoma of known primary (MKP)]. However, 2%–9% of patients are diagnosed with melanoma metastasis of unknown primary (MUP). As MUP and MKP have similar UV-induced mutations and molecular signatures, it is proposed that the primary tumor has regressed completely in patients with MUP. As regression of the primary tumor could be indicative of enhanced recognition of melanoma antigens, we hypothesize that patients with advanced MUP have a better outcome compared with MKP.Patients with advanced MUP from 10 German university hospitals were retrospectively analyzed and matched with MKP based on the type of systemic treatment (BRAF and MEK inhibitors, PD-1 inhibitor monotherapy, combined CTLA-4 and PD-1 inhibitor therapy) therapy line (first or second line) and AJCC stage (IIIC, IV M1a–M1d). Three hundred thirty-seven patients with MUP were identified, and 152 treatments with PD-1 and CTLA-4 inhibitors, 142 treatments with PD-1 inhibitors, and 101 treatments with BRAF and MEK inhibitors were evaluated. Median time to treatment failure was significantly prolonged in patients with MUP treated with PD-1 monotherapy (17 mo, 95% CI: 9–25, P = 0.002) compared with MKP (5 mo, 95% CI: 3.4–6.6), as well as in MUP treated with combined PD-1 and CTLA-4 therapy (11 mo, 95% CI: 4.5–17.5, P < 0.0001) compared with MKP (4 mo, 95% CI: 2.9–5.1) Occurrence of immune-related adverse events and time to treatment failure for patients with BRAF and MEK inhibitors was similar in MKP and MUP. In our multicentre collective, patients with MUP have better outcomes under immunotherapy compared with MKP.
Pediatric melanoma incidence and survival: a fifteen-year nationwide retrospective cohort study in Korea
Authors: Kim Isaac , Oh Jisu , Yoon Siyeoung , Han Man-Yong , Chung Jaiwoo , Jung Younghoon , Lee Hyun-Il , Lee Soonchul
Published: August 2024

The aim of this study was to explore the epidemiology of cutaneous malignant melanoma (CMM) and the associated risk factors influencing its occurrence and survival among Koreans aged <20 years. In this retrospective cohort investigation, we identified cases of incident melanoma diagnosed in Korean patients aged 0–19 years between 2004 and 2019, utilizing the National Health Insurance database. We assessed annual fluctuations in age-adjusted incidence rates and examined 5-year survival rates based on various factors, including sex, age, income level, sun-exposed sites, and the Charlson Comorbidity Index. Of 1160 patients, 51.4% were male and 48.6% were female. The mean age of the patients was 11 years, mostly belonging to the top 25% high-income group. The head and neck regions were the most frequently affected sites. The overall age-adjusted incidence rate of melanoma was 0.22 per 100,000 persons. This rate witnessed a decline of 4.5% annually from 2004 to 2012, followed by a subsequent increase of 12.6% annually from 2012 to 2019. Notably, patients with CMM in low-sun-exposed sites exhibited poorer survival rates compared with those in high-sun-exposed areas (P < 0.05). The incidence of melanomas in children and adolescents in Korea has shown a rising trend since 2012. Further research is needed to investigate the etiology and risk factors in pediatric patients.
Mechanisms of thiazide-induced hypertension treatment: insights from gene expression and histological analysis in malignant stroke-prone spontaneously hypertensive rats
Authors: Ashenagar Mohammad Said , Higashino Toshihide , Matsumoto Akiko , Higashino Hideaki
Published: August 2024

Objective:

Diuretics, including thiazides and thiazide-like drugs, are commonly recommended for treating hypertension, though their precise mechanism of action is not fully understood. This study aimed to investigate the pharmacological effects of trichloromethiazide (TCM) in malignant stroke-prone spontaneously hypertensive rats (M-SHRSP).

Methods:

M-SHRSPs were treated with varying doses of TCM. Prognosis, histological changes, and mRNA expression related to hypertension and stroke were assessed.

Results:

The high-dose TCM group (3%) exhibited significantly lower SBP compared with the untreated group, whereas the low-dose group (0.3%) did not show a significant reduction in SBP. The survival rate was 54% in the low-dose group, whereas all rats in the high-dose group survived without experiencing a stroke by 16 weeks of age. Organ weights in both TCM-treated groups were lower than those in the control group, without severe histological abnormalities, including stroke and sclerosis. Plasma levels of thiobarbituric acid-reactive substances (TBARS) were significantly reduced in both TCM-treated groups. Additionally, 20 genes related to tissue protection, repair, proliferation, maintenance, and function were significantly expressed.

Conclusion:

TCM administration in M-SHRSPs significantly modulated the expression of 20 genes associated with tissue protection and maintenance, and reduced plasma TBARS levels. These findings suggest that TCM, a thiazide diuretic, may protect against tissue impairment in hypertension by modulating gene expression and exhibiting antioxidant activity.
Femtosecond Laser–Assisted Autologous Glueless Simple Limbal Epithelial Transplantation in Unilateral Limbal Stem Cell Deficiency: 12-Month Outcome of the First Clinical Cases
Authors: Malyugin Boris , Svetlana Kalinnikova , Fabian Muller , Werner Bernau , Boris Knyazer , Maksim Gerasimov
Published: August 2024

Purpose:

Surgical treatment of unilateral limbal stem cell deficiency (LSCD) is based on limbal stem cell transplantation. Glueless simple limbal epithelial transplantation (G-SLET) technique implements several limbal micrografts harvested from the healthy eye of the same patient into the peripheral corneal tunnels without the use of fibrin glue and human amniotic membrane.

Methods:

A novel customized algorithm and software for a low-energy femtosecond laser (FSL) were developed and tested using 5 pairs of isolated porcine eyes. FSL-assisted G-SLET modification was assessed in 3 clinical cases of unilateral LSCD caused by chemical burns. Corneal epithelization efficacy, best-corrected visual acuity, corneal epithelial mapping, central corneal thickness, and impression cytology with immunohistochemical examination were evaluated. All patients were followed up for 12 months postoperatively.

Results:

The FSL set for 100% energy and the pattern of 8 nonpenetrating vertical cuts with oblique tunnel portions having variable incision depths and diameter of 8.5 mm and higher were selected for further clinical evaluation. Clinically, stable corneal epithelialization was achieved 2 to 3 weeks after intervention. At the 6-month follow-up, all patients had a healthy corneal epithelium with limbal micrografts visible inside the corneal tunnels. Best-corrected visual acuity markedly improved in 2 cases, but not in the third case with severe corneal stromal scarring. In addition, all patients noted a full-scale reduction in subjective complaints and substantial improvement in their quality of life.

Conclusions:

The FSL-assisted G-SLET is a new technique for autologous limbal stem cell transplantation in patients with unilateral LSCD. It allows the standardization of corneal tunnel localization and dimensions, thereby increasing the safety of the surgical procedure.
A Case of Nasoseptal Flap Reconstruction for Refractory Medial Canthal Fistula
Authors: Wang Kenny Y. , Yu Caroline Y. , Pinheiro-Neto Carlos , Tooley Andrea A.
Published: August 2024

Sino-orbital cutaneous fistulas (SOCFs) are a rare and challenging complication from conditions including granulomatosis with polyangiitis. SOCFs are difficult to manage due to poor vascular supply, compromised tissue, and systemic immunocompromise, which lead to a high rate of recurrence. Given the overall rarity of SOCFs, optimal surgical repair remains controversial, with options ranging from conservative management, onlay grafts, and vascularized flaps. This case report describes a novel one-step approach to SOCF closure using a composite chondral mucosal nasoseptal flap in a patient with a large left medial canthal SOCF that had recurred despite 2 prior attempts at closure including a vascularized paramedian forehead flap. Nasoseptal flaps may provide vascularized mucosal tissue to allow for greater success in closure over traditional, external flaps, and skin grafts.
Comparison of postoperative inflammatory response between natural orifice specimen extraction surgery and conventional laparoscopy in the treatment of colorectal cancer: a meta-analysis and systematic review
Authors: Liu Xinyue , Yuan Xingzhu , Ye Peiling , Yang Jie , Li Ka
Published: August 2024

Purpose:

Natural orifice specimen extraction surgery (NOSES) has attracted attention because of its minimal invasiveness. This meta-analysis compared inflammatory response profiles and infectious complications between colorectal cancer patients treated with NOSES and those treated with conventional laparoscopy.

Methods:

Seven medical databases were searched up to February 2024. The authors included studies that examined changes in the inflammatory response and outcomes in the patients after NOSES surgery. The Cochrane tool and the Newcastle–Ottawa Scale were used to evaluate the quality of the studies. Pooled standardized mean differences and odds ratios with 95% CIs were calculated using either fixed- or random-effects models. Review Manager 5.4 (RevMan 5.4) and the R project were used for the meta-analysis.

Results:

This meta-analysis included 22 studies. Pooled analyses revealed lower tumor necrosis factor-α levels (SMD=−1.34,95% CI [−2.43, −0.25]; Z=2.40, P=0.02 and SMD =−1.49,95% CI [−2.15, −0.82]; Z=4.36, P<0.0001) and C reactive protein levels (SMD=−0.56, 95% CI [−4.17, −2.50]; Z=2.19, P=0.03 and SMD =−1.24,95% CI [−1.77, −0.71]; Z=4.56, P<0.00001) on postoperative day 1 and postoperative day 3 for NOSES than for conventional laparoscopy. Pooled analysis revealed significantly lower interleukin-6 levels in the NOSES group (SMD=−1.88,95% CI [−2.84, −0.93]; Z=3.88, P=0.0001) on postoperative day 3. There were no significant differences in white blood cell count, procalcitonin levels, or the incidence of infectious complications between the two groups.

Conclusions:

NOSES has a superior inflammatory profile and does not increase the incidence of postoperative infectious diseases. The reported results should be validated in a larger population of colorectal cancer patients.
Long-Term Outcomes of Modified Endoscopic Transcanal Approach to Small Acoustic Tumors
Authors: Abdul Halim Riana Kipiani , Lapina Gerard , Shin Seung Ho , Jung Youngrak , Lee Jeong Gum , Moon In Seok
Published: August 2024

Objective

The management options for small acoustic tumors are still controversial, and surgery is indicated in a select number of patients only. This is to avoid unnecessary extensive operations and risk of complications. Endoscopic transcanal approach, which was recently introduced, can be an alternative option to overcome these challenges. We have developed a modified technique for endoscopic transcanal removal of small acoustic tumors with tympanoplasty using tragal cartilage and without the need to harvest abdominal fat for obliteration. There was also no need to do an ear cul-de-sac procedure compared with the previous method. We report the long-term outcomes of this approach.

Study Design

Retrospective review.

Setting

Tertiary hospital.

Patients

Those who were diagnosed with small acoustic tumors between June 2016 and June 2022 were enrolled.

Interventions

Tumor removal via a Modified Endoscopic Transcanal Transpromontorial Approach (mETTA).

Main Outcome Measure

Tumor control rate, closure rate of tympanic membrane, and complications such as cerebrospinal fluid (CSF) leakage and facial palsy were analyzed. Operation time and hospital stay were also analyzed.

Results

Twenty-two patients with a mean age of 55.5 ± 9.4 years were enrolled. Eighteen were vestibular schwannomas (VS), two were intracochlear schwannomas (ICS), and two were with intravestibulocochlear schwannomas (IVCS). Gross total removal was achieved in 21 cases. One had developed significant CSF leakage, and the other patient complicated with permanent facial palsy. The tympanic membrane healed well in all patients, but three patients showed delayed healing until several months and treated conservatively. Mean operation time was 149.6 ± 48.4 minutes, mean hospital stay was 8.9 ± 4.5 days, and mean postoperative follow-up period was 42.0 ± 15.7 months.

Conclusion

Long-term results of modified endoscopic transcanal approach to small acoustic tumors are acceptable and comparable to classical treatments such as translabyrinthine approach or gamma knife radiation. This is an alternative option for smaller tumors warranting surgical removal and maintained cosmetic advantages.
Evaluation of accuracies of large language models in answering clinical questions related to Mediterranean diet on cardiodiabesity
Authors: Chen Chao , Li Xinxin , Luo Hongmiin
Published: August 2024

Objectives:

To explore a method to answer clinical questions (CQs) pertaining to the Mediterranean diet (MedDiet) on cardiodiabesity.

Methods:

We assessed the accuracies of responses provided by large language models (LLMs) to CQs pertaining to the MedDiet on cardiodiabesity. In addition, a comparative analysis of CQs was conducted among various LLMs, including Claude, Gemini, generative pretrained transformer (GPT)-4, Doctor generative language model (GLM), Bencao, and HuatuoGPT, with 1-way analysis of variance, accuracies, and Shannon entropies.

Results:

The results of the analysis of variance show that there are significant discrepancies between the CQ and LLM groups, thereby warranting further analysis. The results of accuracies and Shannon entropies show that GPT-4 and Bencao have the highest accuracy (0.978) in responses to CQs among all 6 LLMs, according to cardiovascular experts.

Conclusions:

We endorse GPT-4 as the preferred model for responding to CQs related to MedDiet on cardiodiabesity. Concurrently, other LLMs also exhibit the potential to respond to these CQs.
Internalized HIV stigma and viral suppression: examining the mediating and moderating roles of substance use and social support
Authors: Crawford Timothy N. , Neilands Torsten B. , Drumright Lydia N. , Fredericksen Rob J. , Johnson Mallory O. , Mayer Kenneth H. , Bamford Laura , Batchelder Abigail W. , Crane Heidi M. , Elopre Latesha , Moore Richard D. , Rosengren A. Lina , Christopoulos Katerina A.
Published: August 2024

Objective:

The aim of this study was to examine the effects of internalized HIV stigma on viral nonsuppression via depressive symptoms, alcohol use, illicit drug use, and medication adherence and investigate whether social support moderates these effects.

Design:

Longitudinal observational clinical cohort of patients in HIV care in the US.

Methods: Data from the CFAR Network for Integrated Clinical Systems (2016–2019) were used to conduct structural equation models (SEM) to test the indirect effects of internalized HIV stigma on viral nonsuppression through depressive symptoms, illicit drug use, alcohol use, and medication adherence. Moderated mediation with an interaction between social support and internalized HIV stigma was examined.

Results:

Among 9574 individuals included in the study sample, 81.1% were men and 41.4% were black, non-Hispanic. The model demonstrated good fit (root mean square error of approximation = 0.028; standardized root means square residual = 0.067). The overall indirect effect was significant [b = 0.058; se  = 0.020; β = 0.048; 95% confidence interval (95% CI) = 0.019–0.098], indicating that internalized HIV stigma's impact on viral nonsuppression was mediated by depressive symptoms, illicit drug use, and medication adherence. An interaction was observed between internalized HIV stigma and social support on alcohol use; however, there was no moderated mediation for any of the mediators.

Conclusion:

Internalized HIV stigma indirectly impacts viral nonsuppression through its effects on depressive symptoms, illicit drug use, and medication adherence. Social support may buffer the impact, but more research is needed. Understanding the pathways through which internalized stigma impacts viral suppression is key to improving health of people with HIV.
Volumetric Bone Changes in Double Barrel Vascularized Fibula Flap Used for Mandibular Reconstruction: A Randomized Clinical Trial
Authors: Okba Hussam Ashraf , Helmy Emad Saeed , Ayad Wael Mohamed , Abdelaziz Omnyia Mohamed
Published: August 2024

Aim:

To assess the volumetric bone changes in double barrel vascularized fibular flap used for mandibular reconstruction using 3D miniplate versus 3D titanium mesh tray.

Materials and Methods:

Twenty patients seeking mandibular reconstruction were selected for this 2-arm parallel randomized clinical trial with a 1:1 allocation ratio. Both groups underwent double-barrel fibula free flap for mandibular reconstruction with fixation of the superior barrel to the inferior barrel using a Titanium mesh (Group A) or a 3D plate (Group B). The primary outcome was volumetric bone changes (immediate to 6 months postoperatively).

Results:

Eleven participants (55%) were females, and 9 participants (45%) were males. The mean age of patients in group A was (28.8±8.9) years, while group B was (30.7±11.4) years. There was a statistically significant difference within each group in the volumetric bone changes with means of −7942.1±1804.8 mm3 and −6288.8±2607.3 for groups A and B, respectively. The difference between both groups was statistically insignificant with the mean of −1653.3±1002.8 mm3. The percentage of mean volumetric change relative to immediate postoperatively for group A was −14.15%, while in group B was −11.01%.

Conclusions:

Both the titanium mesh tray and the 3D plate were effective in the fixation of the superior barrel of the vascularized fibular flap for mandibular reconstruction. There was no difference between both modalities regarding volumetric bone changes.
Anti-HLA Class II Antibodies Are the Most Resistant to Desensitization in Crossmatch-positive Living-donor Kidney Transplantations: A Patient Series
Authors: de Weerd Annelies E. , Roelen Dave L. , Betjes Michiel G.H. , Clahsen-van Groningen Marian C. , Haasnoot Geert W. , Kho Marcia M.L. , Reinders Marlies E.J. , Roodnat Joke I. , Severs David , Karahan Gonca E. , van de Wetering Jacqueline
Published: August 2024

Background.

In HLA-incompatible kidney transplantation, the efficacy of desensitization in terms of anti-HLA antibody kinetics is not well characterized. We present an overview of the course of anti-HLA antibodies throughout plasma exchange (PE) desensitization in a series of crossmatch-positive patients.

Methods.

All consecutive candidates in the Dutch HLA-incompatible kidney transplantation program between November 2012 and January 2022 were included. The eligibility criteria were a positive crossmatch with a living kidney donor and no options for compatible transplantation. Desensitization consisted of 5–10 PE with low-dose IVIg.

Results.

A total of 16 patient-donor pairs were included. Patients had median virtual panel-reactive antibody of 99.58%. Cumulative donor-specific anti-HLA antibody (cumDSA) mean fluorescence intensity (MFI) was 31 399 median, and immunodominant DSA (iDSA) MFI was 18 677 for class I and 21 893 for class II. Median anti-HLA antibody MFI response to desensitization was worse in class II as compared with class I (P < 0.001), particularly for HLA-DQ. Class I cumDSA MFI decreased 68% after 4 PE versus 53% in class II. The decrease between the fifth and the 10th PE sessions was modest with 21% in class I versus 9% in class II. Antibody-mediated rejection occurred in 85% of patients, with the iDSA directed to the same mismatched HLA as before desensitization, except for 3 patients, of whom 2 had vigorous rebound of antibodies to repeated mismatches (RMMs). Rebound was highest (86%) in RMM-DSA with prior grafts removed (transplantectomy n = 7), lower (39%) in non-RMM-DSA (n = 30), and lowest (11%) for RMM-DSA with in situ grafts (n = 5; P = 0.018 for RMM-DSA transplantectomy versus RMM-DSA graft in situ). With a median follow-up of 59 mo, 1 patient had died resulting in a death-censored graft survival of 73%.

Conclusions.

Patients with class II DSA, and particularly those directed against HLA-DQ locus, were difficult to desensitize.
Endogamy and high prevalence of deleterious mutations in India: evidence from strong founder events
Authors: Machha Pratheusa , Gopalan Amirtha , Elangovan Yamini , Mouli Veeravalli Sarath Chandra , Sowpati Divya Tej , Thangaraj Kumarasamy
Published: August 2024

Founder events influence recessive diseases in highly endogamous populations. Several Indian populations have experienced significant founder events and maintained strict endogamy. Genomic studies in Indian populations often lack in addressing clinical implications of these phenomena. We performed whole-exome sequencing of 281 individuals from four South Indian groups to evaluate population-specific disease causing mutations associated with founder events. Our study revealed a high inbreeding rate of 59% across the groups. We identified ∼29.2% of the variants to be exclusive to a single population and uncovered 1,284 novel exonic variants, underscoring the genetic underrepresentation of Indian populations. Among these, 23 predicted as deleterious were found in heterozygous state, suggesting they may be pathogenic in a homozygous state and are common in the endogamous groups. Approximately 40-68% of the identified pathogenic variants showed significantly higher occurrence rates. Pharmacogenomic analysis revealed distinct allele frequencies in CYP450 and non-CYP450 gene variants, highlighting heterogeneous drug responses and associated risks. We report a high prevalence of ankylosing spondylitis in Reddys, linked toHLA-B*27:04allele and strong founder effect. Our findings emphasize the need for expanded genomic research in understudied Indian populations to elucidate disease risk and medical profiles, eventually aiming towards precision medicine and mitigating disease burden.
StrIDR: a database of intrinsically disordered regions of proteins with experimentally resolved structures
Authors: Majila Kartik , Viswanath Shruthi
Published: August 2024

Motivation

Intrinsically disordered regions (IDRs) of proteins exist as an ensemble of conformations, and not as a single structure. Existing databases contain extensive, experimentally derived annotations of intrinsic disorder for millions of proteins at the sequence level. However, only a tiny fraction of these IDRs are associated with an experimentally determined protein structure. Moreover, even if a structure exists, parts of the disordered regions may still be unresolved.

Results

Here we organizeStructures ofIntrinsicallyDisorderedRegions (StrIDR), a database of IDRs confirmedviaexperimental or homology-based evidence, resolved in experimentally determined structures. The database can provide useful insights into the dynamics, folding, and interactions of IDRs. It can also facilitate computational studies on IDRs, such as those using molecular dynamics simulations and/or machine learning.

Availability

StrIDR is available athttps://isblab.ncbs.res.in/stridr. The web UI allows for downloading PDB structures and SIFTS mappings of individual entries. Additionally, the entire database can be downloaded in a JSON format. The source code for creating and updating the database is available athttps://github.com/isblab/stridr.
Metagenomic insights into an enigmatic gammaproteobacterium that is important for carbon cycling in cave ecosystems worldwide
Authors: Jones Daniel S. , Green Katelyn M. , Brown Abigail , Havlena Zoë E. , Best Mackenzie B. , Northup Diana E. , Mainiero Maurizio , Auch Benjamin
Published: August 2024

Caves are windows into the subsurface through which we can directly evaluate the microbiological processes responsible for rock weathering and biogeochemical cycling in more expansive areas of Earth’s subsurface. However, many cave microbial communities are dominated by microorganisms from uncultivated groups with unknown genomic capabilities that cannot be resolved from marker gene surveys alone. An example of this is a genus ofGammaproteobacteriaknown as “wb1-P19”, which are ubiquitous and abundant in rRNA gene surveys from limestone and volcanic caves around the world. We recovered a nearly complete metagenome-assembled genome (MAG) representing a population of wb1-P19 from Lehman Caves in Great Basin National Park, Nevada, USA, and used it to identify additional MAGs representing this group from the Frasassi Caves in Italy and in publicly available databases. Although members of the wb1-P19 group have often been thought to be autotrophs that oxidize inorganic nitrogen compounds, we show that wb1-P19 are actually obligate or facultative methanotrophs capable of aerobic and anaerobic growth. Based on genomic classification, wb1-P19 are members of upland soil cluster γ (USCγ; part of the newly proposed order “CandidatusMethyloligotrophales”), and are likely important for methane consumption and carbon cycling in caves and other subterranean ecosystems globally.
Industrializing yeast as a drug repurposing platform for inherited metabolic diseases
Authors: Thevandavakkam Mathuravani A. , Long Natalie E. , Roel Briannna M. , Kantautas Kristin A. , Zakin Shiri , Duesterberg Van , Perlstein Ethan O.
Published: August 2024

The development of therapies for rare diseases, particularly inherited metabolic disorders (IMDs), faces significant challenges due to the high cost and lengthy timelines involved. This study presents a yeast-based platform for drug repurposing that capitalizes on the remarkable similarity between yeast and human cellular pathways. This platform enables rapid, cost-effective screening of potential therapeutic compounds for rare diseases, offering a quick turnaround compared to traditional drug development processes. Utilizing a TargetMol library of comprising ∼50% nutraceuticals, our pipeline accelerates translation of promising drug repurposing hits into patient observational studies in as little as 6 months. We demonstrate the efficacy of this platform through three case studies in the context of IMDs, showcasing its potential to uncover novel treatments and reduce the time and expense associated with bringing therapies to patients with rare diseases.
tombRaider– improved species and haplotype recovery from metabarcoding data through artefact and pseudogene exclusion
Authors: Jeunen Gert-Jan , Fernandes Kristen , Dowle Eddy , Kroos Gracie C. , Mauvisseau Quentin , Torma Michal , Miller Allison K. , Lamare Miles , Gemmell Neil
Published: August 2024

Environmental DNA metabarcoding has revolutionized ecological surveys of natural systems. By amplifying and sequencing small gene fragments from environmental samples containing complex DNA mixtures, scientists are now capable of exploring biodiversity patterns across the tree of life in a time-efficient and cost-effective manner. However, the accuracy of species and haplotype identification can be compromised by sequence artefacts and pseudogenes. Despite various strategies developed over the years, effective removal of artefacts remains challenging and inconsistent data reporting standards hinder reproducibility in eDNA metabarcoding experiments. To address these issues, we introducetombRaider, an open-source command line software program (https://github.com/gjeunen/tombRaider) and R package (https://github.com/gjeunen/tombRaider_R) to remove artefacts and pseudogenes from metabarcoding data post clustering and denoising.tombRaiderfeatures a modular algorithm capable of evaluating multiple criteria, including sequence similarity, co-occurrence patterns, taxonomic assignment, and the presence of stop codons. We validatedtombRaiderusing various published data sets, including mock invertebrate communities, air eDNA from a zoo, and salmon haplotypes from aquatic eDNA. Our results demonstrate thattombRaidereffectively removed a higher proportion of artefacts while retaining authentic sequences, thus enhancing the accuracy and reliability of eDNA-derived diversity metrics. This user-friendly software program not only improves data quality in eDNA metabarcoding studies, but also contributes to standardised reporting practices, an aspect currently lacking in this emerging research field.
Differential Tractography: A Biomarker for Neuronal Function in Neurodegenerative Disease
Authors: Lewis Connor J. , Vardar Zeynep , Kühn Anna Luisa , Johnston Jean M. , D’Souza Precilla , Gahl William A. , Shazeeb Mohammed Salman , Tifft Cynthia J. , Acosta Maria T.
Published: August 2024

GM1 gangliosidosis is an ultra-rare inherited neurodegenerative lysosomal storage disorder caused by biallelic mutations in theGLB1gene. GM1 is uniformly fatal and has no approved therapies, although clinical trials investigating gene therapy as a potential treatment for this condition are underway. Novel outcome measures or biomarkers demonstrating the longitudinal effects of GM1 and potential recovery due to therapeutic intervention are urgently needed to establish efficacy of potential therapeutics. One promising tool is differential tractography, a novel imaging modality utilizing serial diffusion weighted imaging (DWI) to quantify longitudinal changes in white matter microstructure. In this study, we present the novel use of differential tractography in quantifying the progression of GM1 alongside age-matched neurotypical controls. We analyzed 113 DWI scans from 16 GM1 patients and 32 age-matched neurotypical controls to investigate longitudinal changes in white matter pathology. GM1 patients showed white matter degradation evident by both the number and size of fiber tract loss. In contrast, neurotypical controls showed longitudinal white matter improvements as evident by both the number and size of fiber tract growth. We also corroborated these findings by documenting significant correlations between cognitive global impression (CGI) scores of clinical presentations and our differential tractography derived metrics in our GM1 cohort. Specifically, GM1 patients who lost more neuronal fiber tracts also had a worse clinical presentation. This result demonstrates the importance of differential tractography as an important biomarker for disease progression in GM1 patients with potential extension to other neurodegenerative diseases and therapeutic intervention.
A systematic evaluation of highly variable gene selection methods for single-cell RNA-sequencing
Authors: Zhao Ruzhang , Lu Jiuyao , Zhou Weiqiang , Zhao Ni , Ji Hongkai
Published: August 2024

Background

Selecting highly variable features is a crucial step in most analysis pipelines of single-cell RNA-sequencing (scRNA-seq) data. Despite numerous methods proposed in recent years, a systematic understanding of the best solution is still lacking.

Results

Here, we systematically evaluate 47 highly variable gene (HVG) selection methods, consisting of 21 baseline methods developed based on different data transformations and mean-variance adjustment techniques and 26 hybrid methods developed based on mixtures of baseline methods. Across 19 diverse benchmark datasets, 18 objective evaluation criteria per method, and 5,358 analysis settings, we observe that no single baseline method consistently outperforms the others across all datasets and criteria. However, hybrid methods as a group robustly outperform individual baseline methods. Based on these findings, a new HVG selection approach, mixture HVG selection (mixHVG), that incorporates top-ranked features from multiple baseline methods is proposed as a better solution to HVG selection. An open source R packagemixhvgis developed to enable convenient use of mixHVG and its integration into users’ data analysis pipelines.

Conclusion

Our benchmark study not only provides a systematic comparison of existing methods, leading to a better HVG selection solution, but also creates a pipeline and resource consisting of diverse benchmark data and criteria for evaluating new methods in the future.
Integrating microscopy and transcriptomics from individual uncultured eukaryotic plankton
Authors: Gatt Catherine , Xie Yike , Wahi Kanu , Johansson Emma M. V. , Zanini Fabio
Published: August 2024

Eukaryotic plankton comprises organisms as diverse as diatoms and pelagic larvae, covering a wide spectrum of shapes, molecular compositions, and ecological functions. Plankton research is often approached using either optical methods, especially for taxonomic purposes, or genomics, which excels at describing the biochemistry of microbial communities. This technological dichotomy hampers efforts to link the morpho-optical properties of each species with its genetic and biomolecular makeup, leading to fragmented information and limited reproducibility. Methods to simultaneously acquire multimodal, i.e. optical and genetic, information on planktonic organisms would provide a connection between organismal appearance and function, improve taxonomic prediction, and strengthen ecological analysis. Here we present Ukiyo-e-Seq, an approach to generate paired optical and transcriptomic data from individual eukaryotic plankton. We performed Ukiyo-e-Seq on 66 microscopic organisms from Coogee, NSW, Australia and assembled transcriptomic contigs using a merge-split strategy. While overall phylogenetic heterogeneity spanned hundreds of taxa, diversity in individual wells was low, enabling accurate classification of both microbial plankton and marine larvae. We then combined Ukiyo-e-Seq with AlphaFold 3, a protein language model, and could confidently infer (i) the joint structure and interactions of 34 photosynthesis proteins from a singleChaetocerosdiatom, and (ii) the cellular and developmental functions of novel proteins highly expressed in one trout larva. In summary, Ukiyo-e-Seq is a precise tool to connect morphological and genetic information of eukaryotic plankton.
Development and evaluation of an online training program for palliative care in India
Authors: Passi Varun Raj , Warrier Sreedevi , Balu Rajalekshmi , Sunilkumar MM , Sharma Parth
Published: August 2024

Objective

Palliative care training at the undergraduate level is poor in India. With the need for palliative care rising in India and globally, it is possible to train physicians in resource-limited settings in palliative care via online training programs owing to ease of access and convenience. However, there is limited evidence available from India on the development and implementation of such a training program. This study aims to describe the development of an online training program offered by the Trivandrum Institute of Palliative Sciences (TIPS), Kerala, and the impact of the program on the confidence of physicians in managing various palliative care needs of their patients.

Material and Methods

The course was developed by an interdisciplinary expert team from TIPS. The course content was made keeping in mind the local sociocultural factors in India and was peer-reviewed by two external experts. The program was started in 2018 and updated and revised over the years. Currently, the program has 20 sessions, each lasting for 90 minutes. The course content was disseminated using project-ECHO’s tele mentoring model. To assess the impact of the training program, self-reported change in confidence from twenty-two batches of physicians, trained from January 2020 to August 2023. Feedback from participants was also assessed to identify areas of improvement in the training program.

Results

A total of 1159 physicians were trained during the study period. At the end of the course, 51.2% of the participants completed the evaluation survey and had a statistically significant (p<0.05) improvement in confidence in pain, gastrointestinal symptoms and breathlessness management, morphine prescription, and psychosocial communication. The duration of each session and the entire course was reported to be ideal by 88.6% and 87.9% of participants, respectively.

Conclusion

Our results show that online training can be effectively used to build confidence in physicians in managing various palliative care needs.
Functional maps of a genomic locus reveal confinement of an enhancer by its target gene
Authors: Eder Mathias , Moene Christina J.I. , Dauban Lise , Leemans Christ , van Steensel Bas
Published: August 2024

Genes are often activated by enhancers located at large genomic distances. The importance of this positioning is poorly understood. By relocating promoter-reporter constructs into >1,000 alternative positions within a single locus, we dissected the positional relationship between the mouseSox2gene and its distal enhancer. This revealed an intricate, sharply confined activation landscape, in which the nativeSox2gene occupies an optimal position for its activation. Deletion of the gene relaxes this confinement and broadly increases reporter activity. Surprisingly, the confining effect of theSox2gene is partially conferred by its ∼1 kb coding region. Our local relocation approach provides high-resolution functional maps of a genomic locus and reveals that a gene can strongly constrain the realm of influence of its enhancer.
Comparative analysis of trans-chromosomic rodent models reveals improved somatic hypermutation and class-switch recombination in rats
Authors: Satofuka Hiroyuki , Abe Satoshi , Moriwaki Takashi , Okada Akane , Kazuki Kanako , Hamamichi Shusei , Hiratsuka Masaharu , Hirabayashi Masumi , Nakamura Kazuomi , Sakuma Tetsushi , Yamamoto Takashi , Baba Yoshihiro , Tomizuka Kazuma , Kazuki Yasuhiro
Published: August 2024

Humanized rodent models, especially humanization of genetic/genomic components involved in immunity have significantly advanced our understanding of human immune system. Here, we utilized trans-chromosomic (Tc) technology to generate a TC-mAb rat model that stably harbors a mouse artificial chromosome carrying full-length human immunoglobulin (Ig) heavy and kappa light chain genes (IGHK-NAC) in a rat Ig knockout background. In contrast with TC-mAb mice, serum human IgG concentration was found higher than IgM. Number of lymphocytes was recovered, and B cell population in the spleen was normal. Remarkably, repertoire analysis revealed similarities between the model and human PBMCs; somatic hypermutation and class-switch recombination also more closely resembled humans. Furthermore, immunization resulted in generation of antigen-specific human antibodies. Collectively, our strategy to generate both rat and mouse models through introduction of the identical IGHK-NAC offers unprecedented opportunities to comprehensively evaluate genomic regulation and its outcomes associated with genomic sequences and host-derived protein factors.
A sleep disturbance method by novel objects in the home cage to minimize stress
Authors: Egebjerg Christine , Kolmos Mie Gunni , Abelson Klas , Kornum Birgitte Rahbek
Published: August 2024

Background

The increasing prevalence of low sleep quality is a significant issue, particularly among adolescents, necessitating a deeper understanding of its biological consequences. In sleep research, various protocols are used for sleep deprivation or disturbance, each presenting its own set of confounding factors crucial to consider.

New Method

We developed a standardized seven-day sleep disturbance (SD) protocol using daily four-hour exposures to novel objects to minimize rodent stress. Objects were selected and characterized for wake-promoting properties, and exposure timing was structured to reduce variability and enhance experimental reliability and reproducibility.

Results

During the four hours of SD, the mice were efficiently sleep-deprived on the first and seventh day of SD. Thus, the selected objects efficiently sleep restricted the mice. On the first day of SD, the protocol induced sleep deprivation effect when measured over 24h, but by the seventh day, the mice recovered the sleep loss. Thus, this method is a sub-chronic sleep disturbance and not sleep deprivation. Fecal corticosterone concentrations remained unchanged during the seven days of SD.

Comparison with existing methods

This approach reduced the risk of stress through voluntary rather than forced wakefulness. Previously, novel objects have been exchanged randomly during mouse sleep initiation causing protocol variability and very frequent disturbances. Our protocol minimizes this by introducing the novel object in a structured manner.

Conclusion

We effectively disturbed the sleep of the mice during seven days without inflicting substantial stress. We further demonstrate the value of validating the efficiency of an SD protocol with 24h recordings.

Highlights

Standardized sleep disruption method by object exposure in mice

Mice are sleep-restricted during the four-hour SD intervention all 7 days

Mice habituate to a subchronic sleep deprivation setup by recovering sleep outside of the SD period

Fecal corticosterone samples showed no difference before and after SD intervention
Rapid selection of transgenic mammalian cells via diphtheria toxin resistance
Authors: Scherer David , Honrath Steffen , Leroux Jean-Christophe , Burger Michael
Published: August 2024

The ability to generate stable transgenic mammalian cell lines is crucial to the investigation of gene functions and the production of recombinant proteins. Currently, mammalian cells can be readily transfected in cell culture settings via both viral and nonviral vectors to induce transgene expression. However, there is an unmet need for efficient selection of transfected cells, since current methods involve rather inefficient antibiotic selection protocols or require the coexpression of fluorescent marker proteins, followed by laborious cell sorting procedures. Our aim was to implement a rapid and efficient in situ selection approach for transgene-expressing human cells, using an engineered diphtheria toxin (DT) resistance-based selection, referred to as selecDT. We demonstrated that selecDT is expressed on the surface of modified human cells, provides efficient protection from DT by inactivating its uptake receptor, and, therefore, enables selection. Current antibiotic-based methods require selection periods of more than a week and often achieve only limited cell enrichment. With selecDT, one day of selection is sufficient to obtain nearly 100% enrichment. The DT resistance described herein may thus positively impact biotechnological processes and biomedical research.
Diarylamidine activation of a brachiopod DEG/ENaC/ASIC channel
Authors: Martí-Solans Josep , Børve Aina , Hejnol Andreas , Lynagh Timothy
Published: August 2024

Diarylamidines are a group of widely used small molecule drugs. One common use of diarylamidines is their pharmacological inhibition of ligand-gated cation channels, including tetrameric ionotropic glutamate receptors and trimeric degenerin/epithelial sodium channel channel/acid-sensing ion channels (DEG/ENaC/ASICs). Here, we discover a DEG/ENaC/ASIC channel from the brachiopod (lamp shell)Novocrania anomala, at which diarylamidines act as agonists. The channel is closely related to bile acid-gated, pH-gated, and peptide-gated channels but is not activated by such stimuli. We describe activation of the channel by diminazene, DAPI, and pentamidine, examine several biophysical and pharmacological properties, and briefly explore the molecular determinants of channel activity with site-directed mutagenesis. We term this channel the diarylamidine-activated sodium channel (DiaaNaC).