bluuebunny/crossref_metadata_2025 huggingface dataset:
Revisiting Bipedicled Flaps for Lower Extremity Distal Third Defects
Authors: Bhagat Neel , Berns Jessica , Newsom Keeley , Dawson Steven , Archual Anthony , Christie Brian M. , Weber Erin L. , Hassanein Aladdin H.
Published: June 2023

Background

Lower extremity reconstruction of the distal third of the leg is challenging. Free tissue transfer is the criterion standard. The COVID-19 pandemic encouraged seeking alternatives for resource consuming procedures. Bipedicled flaps are flaps with a dual-source subdermal perfusion. The purpose of this study was to assess outcomes of patients who had bipedicled flaps primary or auxiliary local flap for distal third leg/foot reconstruction.

Methods

A retrospective review of patients undergoing lower extremity reconstruction (2020–2021) was performed. Inclusion criteria were patients older than 18 years with lower extremity wounds secondary to traumatic injury for which bipedicled flaps were used in the reconstruction. Exclusion criteria included lower extremity wounds secondary to peripheral vascular disease or diabetes.

Results

Fourteen patients were included in the study. All patients had distal third of the leg/foot wounds, and 12 patients (87.5%) had concurrent leg fractures. In 8 patients (57.1%), the bipedicled flap was used to decrease the wound size and facilitate another concurrent flap: hemisoleus (21.4%), anterior tibialis muscle turnover (14.3%), medial plantar artery (14.3%), and posterior tibial artery perforator (14.3%). Mean wound size for bipedicle flaps used alone was 42.0 ± 18.3 cm2, whereas wounds that required a bipedicled flap with an additional flap were 69.9 ± 80.8 cm2 (P = 0.187). Two patients had partial flap necrosis (14.3%) but healed their defect. One patient had nonunion (7.1%). Limb salvage rate was 100%.

Conclusions

Bipedicled flaps can be used as an alternative to free flaps in distal third leg/foot defects in select patients. If distal extremity wounds cannot be covered with a bipedicled flap alone, the flap can be used an accessory flap to facilitate reconstruction with other local flaps.
Novel Colon Preparation Method Combining Bowel Cleanser Reduction and Unique Walking
Authors: Koyama Muneyuki , Shiba Hiroaki , Kaneda Yosuke , LuLu Li , Ohya Tomohiko , Takano Yasuhiro , Nishikawa Katsunori , Ohkuma Masahisa , Eto Ken
Published: June 2023

Background and Purpose:

Poor bowel preparation increases the difficulty of colonoscopy and affects lesion detection. In this study, we investigated the usefulness of a new bowel preparation method using polyethylene glycol electrolyte formulation containing ascorbic acid (PEG plus ascorbic acid: PEG-Asc, MOVIPREP) to improve bowel cleansing and shorten preparation time.

Methods:

This was a single-center, retrospective study. In the new method, patients were instructed to take a laxative the day before the examination and PEG1L on the day of the examination. In addition, we instructed the patients to walk, which we designed. The primary endpoints were the degree of bowel cleansing (assessed by the Boston bowel preparation scale, BBPS) and time to the cecum.

Results:

The conventional group reached the cecum in 606.5±225.8 seconds (mean±SD), whereas the introduced group reached the cecum in 500±217.1 seconds, a significantly shorter time (P<0.05). In the BBPS, the score in the introduced group was significantly higher (P<0.01): 6.8±2.14 points in the conventional group and 8.6±0.74 points in the introduction group.

Conclusion:

Pretreatment combining the 1L weight loss method and walking improves bowel cleansing and shortens the time to reach the cecum.
Comparison of Different Weight Meshes in Ventral/Incisional Hernia Repair, the Outcomes of Systematic Review and Meta-analysis
Authors: Li Junsheng , Shao Xiangyu , Cheng Tao
Published: June 2023

Background:

The use of mesh is not without complications. Decreasing the mesh weight with the light-weight (LW) mesh may improve tissue growth and diminish mesh-related complications, yet, clinically, there are conflicting results regarding the influence of different weight meshes in ventral/incisional hernia repair. The aim of the present study is to compare the outcomes of different weight meshes for ventral/incisional hernia repair.

Methods:

The major databases (PubMed, Embase, Springer, and Cochrane Library) were searched, and all studies were published through January 1, 2022, using the keywords “heavy weight” “light weight” “mesh” “ventral hernia” “incisional hernia”. All relevant articles and reference lists in these original studies were also obtained from the above databases.

Results:

Eight trials (4 randomized controlled trials, 3 prospective studies, and 1 retrospective study) containing 1844 patients were included in the present meta-analysis. The pooled results showed that there was a significantly more rate of foreign body perception in the heavy-weight mesh group compared with the LW mesh group (odds ratio = 5.02, 95% CI: 1.05, 24.06). There was no significant difference concerning hernia recurrence, seroma, hematoma, surgical site infection, reoperation rate, chronic pain, quality of life, and hospital stay among different weight mesh groups.

Conclusion:

Different weight meshes showed similar clinical results in ventral/incisional hernia repair, except that, perception of foreign body was reported more frequently in the heavy-weight mesh group as compared with the LW mesh group. However, the long-term hernia recurrence with different weights of meshes needs to be reevaluated considering the relative short-term follow-up in these studies.
Electroconvulsive Therapy in Patients With Cerebral Aneurysms
Authors: Buntting Christopher Shane , Tran David , Fish Charles , Chatha Gurkirat , Jithoo Rondhir
Published: June 2023

Subarachnoid hemorrhage due to cerebral aneurysm rupture is a devastating event with a high mortality and significant morbidity. The safety of patients undergoing electroconvulsive therapy (ECT) in the presence of an aneurysm is not clear and is a cause of anxiety for both health care workers and patients. The present article collated the available evidence related to ECT in the presence of an aneurysm and found that there were no case reports where ECT directly led to the rupture of an aneurysm, although 1 case reported a rupture of an aneurysm between sessions of ECT. The epidemiology of cerebral aneurysms is discussed, as are key clinical considerations related to the care of patients with aneurysms who require ECT.
Dynamics of Depressive and Psychomotor Symptoms During Electroconvulsive Therapy in Older Depressive Patients
Authors: Le Droguene Erwan , Bulteau Samuel , Deschamps Thibault , Thomas-Ollivier Véronique , Brichant-Petitjean Clara , Guitteny Marie , Laurin Andrew , Sauvaget Anne
Published: June 2023

Objective

Electroconvulsive therapy (ECT) is an effective treatment for patients experiencing a major depressive episode, especially older ones. Identification of specific responses within early ECT sessions remains an issue of debate, however. Hence, this pilot study prospectively examined the outcome in terms of depressive signs, symptom by symptom, throughout a course of ECT, concentrating particularly on psychomotor retardation symptoms.

Methods

Nine patients were clinically evaluated several times during the ECT course, before the first session and then weekly (over 3–6 weeks, according to their evolution), by completing the Montgomery-Åsberg Depression Rating Scale (MADRS), the Mini-Mental State Examination test, and the French Retardation Rating Scale for Depression for assessing the severity of psychomotor retardation.

Results

Nonparametric Friedman tests showed significant positive changes in mood disorders during ECT in older depressive patients (mean, −27.3% of initial MADRS total score). Fast improvement in French Retardation Rating Scale for Depression score was observed at t
1 (ie, after 3–4 ECT sessions), whereas a slightly delayed improvement in the MADRS scores was found at t
2 (ie, after 5–6 ECT sessions). Moreover, the scores for items linked to the motor component of psychomotor retardation (eg, gait, postural control, fatigability) were the first to significantly decrease during the first 2 weeks of the ECT course compared with the cognitive component.

Conclusions

Interestingly, participants' concentration on daily functional activities, their interest and fatigability, and their reported state of sadness were the first to progress, representing possible precursor signs of positive patient outcomes after ECT.
Unintended Weight Gain After Treatment of Catatonia With ECT in Autism
Authors: Free Melissa , Pathare Aum , Mahgoub Yassir
Published: June 2023

Catatonia is a syndrome with psychomotor, cognitive, and affective symptoms that has been associated with multiple psychiatric and medical conditions, including autism spectrum disorder. Fluctuations in weight can occur within catatonia by means of poor oral intake, treatment with atypical antipsychotics, and often overlooked psychomotor phenomena. We present a case of a patient with autism spectrum disorder and excessive psychomotor activity due to catatonia who initially experienced weight loss despite maintenance of oral intake and required increased caloric intake to maintain her weight. She was treated with electroconvulsive therapy. After the psychomotor phenomena associated with catatonia reduced, she gained 10 lb (4.5 kg) despite no further alterations to medications or diet. This case demonstrates that excessive psychomotor activity seen in catatonia may increase energy expenditure to the severity of altering caloric requirements and that weight is a salient biomarker to be monitored in catatonia, especially with those who have limited communication abilities.
Subanesthetic Dose of Ketamine Administered Before Each Electroconvulsive Therapy Session Improves Antidepressant and Sleep Quality Outcomes
Authors: Dong Jun , Min Su , Chen Qibing , Qiu HaiTang , Ren Li
Published: June 2023

Objectives

The main purpose of this trial is to explore the effects of subanesthetic dose of ketamine on sleep quality and symptoms in patients with major depressive disorder undergoing bitemporal electroconvulsive therapy (ECT).

Methods

Seventy-one patients with major depressive disorder and sleep disturbance were randomly divided into 2 groups, namely, the ECT without ketamine group (group ES), receiving routine ECT and saline (3 mL) at each ECT session, and the ECT-assisted ketamine group (group KS), which received ECT and ketamine (3 mL) at each ECT session. The 24 Hamilton Depression Rating Scale was used to assess depressive symptoms and the Chinese Pittsburgh Sleep Quality Index was used to evaluate sleep quality.

Results

The patients in group KS required shorter ECT treatment sessions. Patients in group ES had lower sleep efficiency, longer sleep latency, and required more sleep medication than patients in group KS at the end of the ECT course.

Conclusions

Subanesthetic dose of ketamine improved sleep quality and enhanced ECT therapeutic effects in patients with sleep disturbance.
Linking critical thermal maximum to mortality from thermal stress in a cold-water frog
Authors: Cicchino Amanda S. , Ghalambor Cameron K. , Funk W. Chris
Published: June 2023

Estimates of organismal thermal tolerance are frequently used to assess physiological risk from warming, yet the assumption that these estimates are predictive of mortality has been called into question. We tested this assumption in the cold-water-specialist frog,
Ascaphus montanus
. For seven populations, we used dynamic experimental assays to measure tadpole critical thermal maximum (CTmax) and measured mortality from chronic thermal stress for 3 days at different temperatures. We tested the relationship between previously estimated population CTmax and observed mortality, as well as the strength of CTmax as a predictor of mortality compared to local stream temperatures capturing varying timescales. Populations with higher CTmax experienced significantly less mortality in the warmest temperature treatment (25°C). We also found that population CTmax outperformed stream temperature metrics as the top predictor of observed mortality. These results demonstrate a clear link between CTmax and mortality from thermal stress, contributing evidence that CTmax is a relevant metric for physiological vulnerability assessments.
Functional differentiation of Sec13 paralogues in the euglenozoan protists
Authors: Faktorová Drahomíra , Záhonová Kristína , Benz Corinna , Dacks Joel B. , Field Mark C. , Lukeš Julius
Published: June 2023

The β-propeller protein Sec13 plays roles in at least three distinct processes by virtue of being a component of the COPII endoplasmic reticulum export vesicle coat, the nuclear pore complex (NPC) and the Seh1-associated (SEA)/GATOR nutrient-sensing complex. This suggests that regulatory mechanisms coordinating these cellular activities may operate
via
Sec13. The NPC, COPII and SEA/GATOR are all ancient features of eukaryotic cells, and in the vast majority of eukaryotes, a single Sec13 gene is present. Here we report that the Euglenozoa, a lineage encompassing the diplonemid, kinetoplastid and euglenid protists, possess two Sec13 paralogues. Furthermore, based on protein interactions and localization studies we show that in diplonemids Sec13 functions are divided between the Sec13a and Sec13b paralogues. Specifically, Sec13a interacts with COPII and the NPC, while Sec13b interacts with Sec16 and components of the SEA/GATOR complex. We infer that euglenozoan Sec13a is responsible for NPC functions and canonical anterograde transport activities while Sec13b acts within nutrient and autophagy-related pathways, indicating a fundamentally distinct organization of coatomer complexes in euglenozoan flagellates.
Antimicrobial and quorum sensing inhibitory activity of epiphytic bacteria isolated from the red alga Halymenia durvillei
Authors: Padayao Mary Hannah Rose , Padayao Francis Reuben Paul , Patalinghug Jenny Marie , Raña Gem Stephen , Yee Jonie , Geraldino Paul John , Quilantang Norman
Published: June 2023

Halymenia durvillei is a red alga that is commonly utilized in the Philippines as food and as a source of high value natural products for industrial applications. However, there are no studies regarding the microbial community associated with H. durvillei and its potential applications. This study aimed to isolate and identify the epiphytic bacteria of H. durvillei and determine their antimicrobial and quorum sensing inhibitory (QSI) effects. The thalli of H. durvillei were collected at the shores of Santa Fe, Bantayan, Cebu, Philippines. Bacterial isolates were identified using 16S rRNA, and their ethyl acetate (EtOAc) extracts were subjected to antimicrobial susceptibility tests against representative species of yeast, Gram-negative, and Gram-positive bacteria. Their QSI activity against Chromobacterium violaceum was also determined. Fourteen distinct bacterial colonies belonging to four genera, namely, Alteromonas (3), Bacillus (5), Oceanobacillus (1), and Vibrio (5) were successfully isolated and identified. All fourteen bacterial isolates exhibited antibacterial effects. EPB9, identified as B. safensis, consistently showed the strongest inhibition against Escherichia coli, Staphylococcus aureus, and S. epidermidis having minimum inhibitory concentrations (MIC) ranging from 0.0625 – 1.0 mg mL-1. In contrast, all fourteen isolates showed weak antifungal effects. Both B. safensis (EPB 9) and B. australimaris (EPB15) exhibited QSI effects at 100 mg mL-1 showing opaque zones of  3.1 ± 0.9 mm and 3.8 ± 0.4 mm, respectively. This study is the first to isolate and identify the distinct microbial epiphytic bacterial community of H. durvillei and its potential as an abundant resource for new antibacterial and QSI bioactives.
RSYD-BASIC: a bioinformatics pipeline for Routine Sequence analYsis and Data processing of BActerial iSolates for clInical miCrobiology
Authors: Steinke Kat , Thomsen Karina Gravgaard , Hoegh Silje Vermedal , Larsen Sanne Løkkegaard , Kubel Vilhelmsen Karina , Jensen Thøger Gorm , Skov Marianne Nielsine , Sydenham Thomas Vognbjerg
Published: June 2023

Whole genome sequencing of bacterial isolates is increasingly becoming routine in clinical microbiology; however, subsequent analysis often needs to be started by a bioinformatician even for comprehensive pipelines.  With the RSYD-BASIC pipeline, we present a reads-to-results analysis pipeline operated by non-expert users that has already yielded clinically relevant results.
Identification of further variation at the lipooligosaccharide outer core locus in Acinetobacter baumannii genomes and extension of the OCL reference sequence database for Kaptive
Authors: Sorbello Bianca M. , Cahill Sarah M. , Kenyon Johanna J.
Published: June 2023

The outer core locus (OCL) that includes genes for the synthesis of the variable outer core region of the lipooligosaccharide (LOS) is one of the key epidemiological markers used for tracing the spread of

Acinetobacter baumannii

, a bacterial pathogen of global concern. In this study, we screened 12 476 publicly available

A. baumannii

genome assemblies for novel OCL sequences, detecting six new OCL types that were designated OCL17–OCL22. These were compiled with previously characterized OCL sequences to create an updated version of the

A. baumannii

OCL reference database, providing a total of 22 OCL reference sequences for use with the bioinformatics tool Kaptive. Use of this database against the 12 476 downloaded assemblies found OCL1 to be the most common locus, present in 73.6 % of sequenced genomes assigned by Kaptive with a match confidence score of good or above. OCL1 was most common amongst isolates belonging to sequence types (STs) ST1, ST2, ST3 and ST78, all of which are over-represented clonal lineages. The highest level of diversity in OCL types was found in ST2, with eight different OCLs identified. The updated OCL reference database is available for download from GitHub (https://github.com/klebgenomics/Kaptive; under version v. 2.0.5), and has been integrated for use on Kaptive-Web (https://kaptive-web.erc.monash.edu/) and PathogenWatch (https://pathogen.watch/), enhancing current methods for

A. baumannii

strain identification, classification and surveillance.
A Mathematical Framework for Understanding Recognition Systems
Authors: Brima Yusuf
Published: June 2023

Recognition plays a crucial role in the formation of social bonds, mate selection, kin selection and survival across species. However, a unifying framework for understanding recognition systems in biology is lacking. We, therefore, propose a theoretical framework for biological recognition utilizing basic principles from category theory, information theory, dynamical systems modeling and optimization theory. We define the two types of recognition, individual recognition (IR) and class-level recognition (CR), asfunctorsbetween categories ofstimuliandresponses. IR producesuniqueresponses for each individual, while CR producessharedresponses for multiple individuals of the same class. We identify five conditions –universality, low entropy, unfalsifiability, uniform convergenceandcognitive limit– that must hold for robust IR systems, which we term “signature systems.” Further, we model signature systems asattractor stateswith perspectives from both statistical information processing and dynamical systems. Our framework provides a basis for advancing understanding of the mechanisms underlying biological recognition and its implications for communication and behavior. Overall, the mathematical conceptualization of IR provides a basis for advancing our understanding of communication and the evolution of language.
Pre-trained Multimodal Large Language Model Enhances Dermatological Diagnosis using SkinGPT-4
Authors: Zhou Juexiao , He Xiaonan , Sun Liyuan , Xu Jiannan , Chen Xiuying , Chu Yuetan , Zhou Longxi , Liao Xingyu , Zhang Bin , Gao Xin
Published: June 2023

Large language models (LLMs) are seen to have tremendous potential in advancing medical diagnosis recently. However, it is important to note that most current LLMs are limited to text interaction alone. Meanwhile, the development of multimodal large language models for medical diagnosis is still in its early stages, particularly considering the prevalence of image-based data in the field of medical diagnosis, among which dermatological diagnosis is a very important task as skin and subcutaneous diseases rank high among the leading contributors to the global burden of nonfatal diseases. Inspired by current state-of-the-art multimodal large language models, we present SkinGPT-4, which is the world’s first interactive dermatology diagnostic system based on multimodal large language models. To implement SkinGPT-4, we have designed a new framework that aligned a pre-trained vision transformer with a large language model named Falcon-40B-Instruct, which is based on Falcon. To train SkinGPT-4, we have collected an extensive collection of skin disease images (comprising 52,929 publicly available and proprietary images) along with clinical concepts and doctors’ notes and designed a two-step training strategy. To demonstrate the robustness of SkinGPT-4, we have conducted quantitative evaluations on 150 real-life cases, which were independently reviewed by certified dermatologists. With SkinGPT-4, users could upload their own skin photos for diagnosis, and the system could autonomously evaluate the images, identifies the characteristics and categories of the skin conditions, performs in-depth analysis, and provides interactive treatment recommendations. Meanwhile, SkinGPT-4’s local deployment capability and commitment to user privacy also render it an appealing choice for patients. Though SkinGPT-4 is not a substitute for doctors, it could enhance users’ comprehension of their medical conditions, facilitate improve communication between patients and doctors, expedite the diagnostic process for dermatologists, facilitate triage, and potentially promote human-centred care and healthcare equity in underdeveloped areas. In summary, SkinGPT-4 represents a significant leap forward in the field of dermatology diagnosis in the era of large language models and a valuable exploration of multimodal large language models in medical diagnosis.
Convergent Insulin and TGF-β signalling drives cancer cachexia by promoting aberrant fatbody ECM accumulation in aDrosophilatumour model
Authors: Bakopoulos Daniel , Golenkina Sofia , Dark Callum , Christie Elizabeth L , Sánchez-Sánchez Besaiz J. , Stramer Brian M. , Cheng Louise Y
Published: June 2023

Cancer cachexia is a wasting disease suffered by advanced stage cancer patients and ultimately causes ∼30% of cancer mortalities. Clinical observations have shown that extracellular matrix (ECM) remodelling which leads to fibrosis in the adipose tissue is a key feature of cancer cachexia. However, the molecular regulators of adipose ECM remodelling are not known and how this leads to muscle wasting is unclear. In this study, using aDrosophilacachexia model, we found that in the adipose tissue of both wildtype and tumour bearing animals, insulin and TGF-β signalling converge via a BMP antagonistshort gastrulation(sog) to regulate ECM remodelling. In tumour bearing animals, the aberrant ECM accumulation in the fatbody, contributes towards muscle detachment by preventing ECM secretion and subsequently depleting muscles of fatbody-secreted ECM proteins. Strikingly, activation of insulin signalling, inhibition of TGF-β signalling, or modulation of ECM secretion via SPARC or Rab10 in the fatbody, was able to rescue tissue wasting in the presence of tumour. Together, our study highlights the importance of adipose ECM remodelling in the context of cancer cachexia.
Alterations of lipid homeostasis in serum and white adipose tissue in morbid obese patients are partly reversed by the bariatric surgery
Authors: Sinturel Flore , Chera Simona , Brulhart-Meynet Marie-Claude , Montoya Jonathan Paz , Lefai Etienne , Jornayvaz François R. , D’Angelo Giovanni , Jung Minoa Karin , Pataky Zoltan , Riezman Howard , Dibner Charna
Published: June 2023

Gastric Bypass surgery (GBS) represents a well-established approach to counteract human morbid obesity and its related comorbidities in modern countries. Beside its beneficial effect on weight loss and glucose homeostasis, emerging evidence suggests that GBS impacts on the circulating levels of phospho- and sphingolipids. However, long-term effects of GBS on lipid metabolism have not been explored. Thereby, we aimed to unveil to what extent GBS improves lipid homeostasis in serum and tissues from morbid obese individuals.

To investigate alterations in lipidomic signatures associated with massive weight loss following GBS in morbid obese patients, we employed direct infusion tandem mass spectrometry (MS) allowing to quantify a wide range of lipid metabolites in serum and subcutaneous adipose tissue (SAT) samples. Systematic lipidomic analyses were conducted in samples collected in a longitudinal cohort of patients (cohort 1, n = 11) prior to GBS, and one year following the surgery. These novel data were cross compared with our recent lipidomic analyses conducted by the same approach in an independent cohort of morbid obese patients and lean controls, where serum and visceral adipose tissue (VAT) lipids were analysed (cohort 2, n = 39).

Over 400 phospholipid and sphingolipid species have been quantified in serum and SAT (cohort 1), allowing to establish detailed lipidomic signatures associated with morbid obesity in a tissue-specific manner. Concomitant with weight loss and improvement of metabolic parameters, a massive rearrangement of lipid metabolites was observed one year following GBS. Strikingly, a substantial reduction of ceramide levels and increased amount of hexosylceramides were detected in both serum and SAT. The comparison of these new lipidomic profiles with the serum and VAT lipidomes established from lean and morbid obese subjects (cohort 2) revealed that GBS partly restored the lipid alterations associated with morbid obesity.

Our study provides the first systematic analysis of the long-term lipid homeostasis modifications upon GBS in humans SAT and serum and demonstrates that lipid metabolism alterations associated with morbid obesity might be partly reversed by GBS.

The research protocol was registered with the Protocol Registration and Results System atClinicalTrial.gov[NCT03029572].
Detection of multidrug resistant organisms of concern includingS. maltophiliaandB. cepaciaat a referral hospital in Kenya
Authors: Kimani Racheal , Maina Patrick , Kamita Moses , Mbogo David , Mutai Winnie , Ayodo Charchil , Suliman Essuman , Kanoi Bernard N. , Gitaka Jesse
Published: June 2023

It is important to monitor of antibiotic susceptibility patterns of bacteria in clinical settings periodically to ascertain the current trends as well as re-establish empirical therapy. This study aimed to determine bacterial contaminants and their antimicrobial susceptibility patterns from medical equipment, inanimate surfaces and clinical samples isolated from Thika Level V Hospital (TLVH). Three hundred and five samples were collected and comprised of urine, pus swabs, catheter swabs, stool and environmental samples. Bacterial identification and antimicrobial susceptibility testing were done on VITEK 2 and disc diffusion respectively.

Coagulase negativeStaphylococci(28 /160, 17.5%) were the most isolated species from patients followed byE. coli(22 /160 13.8%) andS. aureus(22/160, 13.8%). The bed rail was the most contaminated surface withS. aureusat (6/42)14.2%. The clinical sample that yielded the highest number of pathogens was pus (92/160). Trauma patients had the largest proportion of isolates (67/160, 41.8%). Bacteria recovered from this study demonstrated high levels of resistance especially enteric bacteria. Extended Spectrum Beta Lactamase phenotype was noted in 29/44 (65.9%) enteric isolates. Although ESBL genetic confirmatory studies are needed, this study shows that there is an urgent need for actions that mitigate the spread of antibiotics resistant bacteria.
Objective Monitoring of Loneliness Levels using Smart Devices: A Multi-Device Approach for Mental Health Applications
Authors: Jafarlou Salar , Azimi Iman , Lai Jocelyn , Wang Yuning , Labbaf Sina , Nguyen Brenda , Qureshi Hana , Marcotullio Christopher , Borelli Jessica L. , Dutt Nikil D. , Rahmani Amir M.
Published: June 2023

Loneliness is linked to wide ranging physical and mental health problems, including increased rates of mortality. Understanding how loneliness manifests is important for targeted public health treatment and intervention. With advances in mobile sending and wearable technologies, it is possible to collect data on human phenomena in a continuous and uninterrupted way. In doing so, such approaches can be used to monitor physiological and behavioral aspects relevant to an individual’s loneliness. In this study, we proposed a method for continuous detection of loneliness using fully objective data from smart devices and passive mobile sensing. We also investigated whether physiological and behavioral features differed in their importance in predicting loneliness across individuals. Finally, we examined how informative data from each device is for loneliness detection tasks. We assessed subjective feelings of loneliness while monitoring behavioral and physiological patterns in 30 college students over a 2-month period. We used smartphones to monitor behavioral patterns (e.g., location changes, type of notifications, in-coming and out-going calls/text messages) and smart watches and rings to monitor physiology and sleep patterns (e.g., heart-rate, heart-rate variability, sleep duration). We also collected participants’ loneliness feeling scales multiple times a day through a questionnaire app on their phone. Using the data collected from their devices, we trained a random forest machine learning based model to detect loneliness levels. We found support for loneliness prediction using a multi-device and fully-objective approach. Furthermore, behavioral data collected by smartphones generally were the most important features across all participants. The study provides promising results for using objective data to monitor mental health indicators, which could provide a continuous and uninterrupted source of information in mental healthcare applications.
Cognitive Dynamics Estimation: A whole-brain spatial regression paradigm for extracting the temporal dynamics of cognitive processes
Authors: Koyama Yutaro , Yamamoto Tetsuya , Hirayama Jun-ichiro , Jimura Koji , Sadato Norihiro , Chikazoe Junichi
Published: June 2023

Functional MRI (fMRI) has been instrumental in understanding how cognitive processes are spatially mapped in the brain, yielding insights about brain regions and functions. However, in case the orthogonality of behavioral or stimulus timing is not guaranteed, the estimated brain maps fail to dissociate each cognitive process, and the resultant maps become unstable. Also, the brain mapping exercise can not provide temporal information on the cognitive process. Here we propose a qualitatively different approach to fMRI analysis, named Cognitive Dynamics Estimation (CDE), that estimates how multiple cognitive processes change over time even when behavior or stimulus logs are unavailable. This method transposes the conventional brain mapping; the brain activity pattern at each time point is subject to regression analysis with data-driven maps of cognitive processes as regressors, resulting in the time series of cognitive processes. The estimated time series captured the fluctuation of intensity and timing of cognitive processes on a trial-by-trial basis, which conventional analysis could not capture. Notably, the estimated time series predicted participants’ cognitive ability to perform each psychological task. As an addition to our fMRI analytic toolkit, these results suggest the potential for CDE to elucidate underexplored cognitive phenomena, especially in the temporal domain.

Highlights

We propose a novel fMRI analysis that are equivalently effective to the brain mapping approach

The temporal dynamics of multiple cognitive processes were captured on a trial-by-trial basis.

This analysis can be applied data-driven even when the researchers do not have any hypothesis about what kind of cognitive processes are recruited in the task.

This analysis can be applied even when the cognitive processes are strongly correlated in the temporal domain.

The estimated temporal dynamics well predicted individuals’ cognitive ability required for each task.
Improved short-channel regression for mapping resting-state functional connectivity networks using functional near-infrared spectroscopy
Authors: Novi S. L. , Abdalmalak A. , Kazazian K. , Norton L. , Debicki D. B. , Mesquita R. C. , Owen A. M.
Published: June 2023

Resting-state functional connectivity (rsFC) is an attractive biomarker of brain function that can vary with brain injury. The simplicity of resting-state protocols coupled with the main features of functional near-infrared spectroscopy (fNIRS), such as portability and versatility, can facilitate the monitoring of unresponsive patients in acute settings at the bedside. However, accurately mapping rsFC networks is challenging due to signal contamination from non-neural components, such as scalp hemodynamics and systemic physiology. Physiological noise may be mitigated through the use of short channels which may be able to provide sufficient information to eliminate the need for additional measurement devices, decreasing the complexity of the experimental setup. To this end, we examined the extent to which systemic physiology is embedded in the short-channel data and improved short-channel regression to account for temporal heterogeneity in the scalp hemodynamics. Our findings indicate that using temporal shifts in the short-channel data increases the agreement, by 70% on average, between short-channel regression and regression that includes short channels and physiological recordings. Overall, this method decreases the need for additional physiological recordings when mapping rsFC networks, providing a viable alternative when such measurements are not available or feasible.
Involvement of a serotonin/GLP-1 circuit in adolescent isolation-induced diabetes
Authors: Kolling Louis J. , Khan Kanza , Balasubramanian Nagalakshmi , Guo Deng-Fu , Rahmouni Kamal , Marcinkiewcz Catherine A.
Published: June 2023

In 2020, stay-at-home orders were implemented to stem the spread of SARS-CoV-2 worldwide. Social isolation can be particularly harmful to children and adolescents—during the pandemic, the prevalence of obesity increased by ∼37% in persons aged 2-19. Obesity is often comorbid with type 2 diabetes, which was not assessed in this human pandemic cohort. Here, we investigated whether male mice isolated throughout adolescence develop type 2 diabetes in a manner consistent with human obesity-induced diabetes, and explored neural changes that may underlie such an interaction. We find that isolating C57BL/6J mice throughout adolescence is sufficient to induce type 2 diabetes. We observed fasted hyperglycemia, diminished glucose clearance in response to an insulin tolerance test, decreased insulin signaling in skeletal muscle, decreased insulin staining of pancreatic islets, increased nociception, and diminished plasma cortisol levels compared to group-housed control mice. Using Promethion metabolic phenotyping chambers, we observed dysregulation of sleep and eating behaviors, as well as a time-dependent shift in respiratory exchange ratio of the adolescent-isolation mice. We profiled changes in neural gene transcription from several brain areas and found that a neural circuit between serotonin-producing and GLP-1-producing neurons is affected by this isolation paradigm. Overall, spatial transcription data suggest decreased serotonin neuron activity (via decreased GLP-1-mediated excitation) and increased GLP-1 neuron activity (via decreased serotonin-mediated inhibition). This circuit may represent an intersectional target to further investigate the relationship between social isolation and type 2 diabetes, as well as a pharmacologically-relevant circuit to explore the effects of serotonin and GLP-1 receptor agonists.

Article Highlights

Isolating C57BL/6J mice throughout adolescence is sufficient to induce type 2 diabetes, presenting with fasted hyperglycemia.

Adolescent-isolation mice have deficits in insulin responsiveness, impaired peripheral insulin signaling, and decreased pancreatic insulin production.

Transcriptional changes across the brain include the endocannabinoid, serotonin, and GLP-1 neurotransmitters and associated receptors.

The neural serotonin/GLP-1 circuit may represent an intersectional target to further investigate the relationship between social isolation and type 2 diabetes. Serotonin-producing neurons of adolescent-isolation mice produce fewer transcripts for the GLP-1 receptor, and GLP-1 neurons produce fewer transcripts for the 5-HT1Aserotonin receptor.
Sustained growth and rapid dispersal of chitin-associated marine bacteria
Authors: Guessous Ghita , Patsalo Vadim , Balakrishnan Rohan , Çağlar Tolga , Williamson James R. , Hwa Terence
Published: June 2023

Many biogeochemical functions involve bacteria utilizing solid substrates. However, little is known about the coordination of bacterial growth with the kinetics of attachment to and detachment from such substrates. In this quantitative study ofVibrio sp. 1A01growing on chitin particles, we reveal the heterogeneous nature of the exponentially growing culture, comprised of two co-existing subpopulations: a minority replicating on chitin particles and a non-replicating majority which was planktonic. This partition resulted from a high rate of cell detachment from particles. Despite high detachment, sustained exponential growth of cells on particles was enabled by the enrichment of extra-cellular chitinases excreted and left behind by detached cells. The “inheritance” of these chitinases sustains the colonizing subpopulation despite its reduced density. This simple mechanism helps to circumvent a tradeoff between growth and dispersal, allowing particle-associated marine heterotrophs to explore new habitats without compromising their fitness on the habitat they have already colonized.
Construction of a multi-tissue cell atlas reveals cell-type-specific regulation of molecular and complex phenotypes in pigs
Authors: Chen Lijuan , Li Houcheng , Teng Jinyan , Wang Zhen , Qu Xiaolu , Chen Zhe , Cai Xiaodian , Zeng Haonan , Bai Zhonghao , Li Jinghui , Pan Xiangchun , Yan Leyan , Wang Fei , Lin Lin , Luo Yonglun , Sahana Goutam , Lund Mogens Sandø , Ballester Maria , Crespo-Piazuelo Daniel , Karlskov-Mortensen Peter , Fredholm Merete , Clop Alex , Amills Marcel , Loving Crystal , Tuggle Christopher K. , Madsen Ole , Li Jiaqi , Zhang Zhe , Liu George E. , Jiang Jicai , Fang Lingzhao , Yi Guoqiang
Published: June 2023

The systematic characterization of cellular heterogeneity among tissues and cell-type-specific regulation underlying complex phenotypes remains elusive in pigs. Within the Pig Genotype-Tissue Expression (PigGTEx) project, we present a single-cell transcriptome atlas of adult pigs encompassing 229,268 high-quality nuclei from 19 tissues, annotated to 67 major cell types. Besides cellular heterogeneity within and across tissues, we further characterize prominent tissue-specific features and functions of muscle, epithelial, and immune cells. Through deconvoluting 3,921 bulk RNA-seq samples from 17 matching tissues, we dissect thousands of genetic variants with cell-type interaction effects on gene expression (ieQTL). By colocalizing these ieQTL with variants associated with 268 complex traits, we provide new insights into the cellular mechanisms behind these traits. Moreover, we highlight that orthologous genes with cell-type-specific regulation in pigs exhibit significant heritability enrichment for some human complex phenotypes. Altogether, our work provides a valuable resource and highlights novel insights in cellular regulation of complex traits for accelerating pig precision breeding and human biomedical research.
The SOCE system is critical for membrane bleb formation to drive avian primordial germ cell migration
Authors: Morita Mizuki , Morimoto Manami , Teramoto Takayuki , Ikenouchi Junichi , Atsuta Yuji , Saito Daisuke
Published: June 2023

Amoeboid cell migration is driven by the specialized cell protrusion, membrane bleb. A recentin vitroanalysis of bleb formation using a cancer cell line showed that store-operated calcium entry (SOCE)-mediated local elevation of Ca2+concentration triggers bleb formation, but it remains unknown how commonly this system is utilized in the bleb formation and bleb-driven cell migrationin vivo. We demonstrate with avian primordial germ cell (PGC) model that that chick PGCs use SOCE, triggered by stem cell factor (SCF), to induce bleb formation and that it is essential forin vivomigration including trans-endothelial and mesenchymal cell migration. Our discovery also provides insight into the correlation between cancer metastasis/invasion and SOCE-mediated bleb formation.
Saccharomyces cerevisiaeDmo2p is involved in the mitochondrial copper metabolism and is required for the stability of newly translated Cox2p
Authors: Soares Maria Antônia Kfouri Martins , Franco Letícia Veloso Ribeiro , Chagas Jhulia Almeida Clarck , Gomes Fernando , Barros Mário H.
Published: June 2023

Based on available platforms ofSaccharomyces cerevisiaemitochondrial proteome and other high throughput studies, we identified the yeast geneDMO2with a profile of genetic and physical interactions that indicate a putative role in mitochondrial respiration. Dmo2p is a homolog to human DMAC1 with two conserved cysteines in a Cx2C motif. Here, we localized Dmo2p in the mitochondrial inner membrane with the conserved cysteines facing the intermembrane space. The observed phenotypes of thedmo2null mutant indicate a general function in cellular stress response; the mutant displayed poor growth on non-fermentative media at 37°C, and in oleate, it is more sensitive to heat and oxidative stress while its overexpression confers resistance to some of the tested stressors. Dmo2p topology and modeled structure suggested a functional redox role for the Cx2C motif sustained by site-directed mutagenesis of both cysteine residues. The respiratory deficiency ofdmo2mutants at 37°C led to a reduction in cytochromecoxidase activity (COX) and the formation ofbc1-COX supercomplexes; we also observed a rapid turnover of Cox2p, the subunit two of the cytochromecoxidase complex that harbors the binuclear CuAcenter. Moreover, Dmo2p co-immunoprecipitated with Cox2p and components of CuAcenter maturation such as Sco1p and Sco2p; and finally,DMO2overexpression can suppresscox23respiratory deficiency, a mutant that has the mitochondrial copper homeostasis impaired. Overall, our data suggest that Dmo2p is required for Cox2p maturation, potentially by aiding proteins involved in copper transport and incorporation into Cox2p.
Performance analysis of conventional and AI-based variant callers using short and long reads
Authors: Abdelwahab Omar , Belzile François , Torkamaneh Davoud
Published: June 2023

The accurate detection of variants is essential for genomics-based studies. Currently, there are various tools designed to detect genomic variants, however, it has always been a challenge to decide which tool to use, especially when various major genome projects have chosen to use different tools. Thus far, most of the existing tools were mainly developed to work on short-read data (i.e., Illumina); however, other sequencing technologies (e.g. PacBio, and Oxford Nanopore) have recently shown that they can also be used for variant calling. In addition, with the emergence of artificial intelligence (AI)-based variant calling tools, there is a pressing need to compare these tools in terms of efficiency, accuracy, computational power, and ease of use. In this study, we evaluated the most widely used conventional and AI-based variant calling tools (BCFTools, GATK4, Platypus, DNAscope, and DeepVariant) in terms of accuracy and computational cost using both short-read and long-read data derived from three different sequencing technologies for the same set of samples from the Genome In A Bottle (GIAB) project. The analysis showed that AI-based variant calling tools supersede conventional ones for calling SNVs and INDELs using both long and short reads. In addition, we demonstrate the advantages and drawbacks of each tool while ranking them in each aspect of these comparisons. This study provides best practices for variant calling using AI-based and conventional variant callers with different types of sequencing data.
How formate dehydrogenase-lacking acetogenClostridium bovifaecisutilize formate as the sole carbon source for its acetogenic growth?
Authors: Guan Ziwei , Fu Bo , Conrad Ralf , Qian Qingqing , Han Dongfei , Liu Hongbo , Liu He
Published: June 2023

Little is known about the growth of formate dehydrogenase-lacking acetogen on formate as sole carbon source. Here, we analyzed formate metabolism inClostridium bovifaecisstrain BXX using different concentrations of formate. The results show thatC. bovifaecisconverted formate (11.5-96 mM) into acetate with molar ratio of 2.0:1∼2.6:1 by using L-cysteine in the anaerobic medium as electron source according to the stoichiometry of acetogenesis. Genome analysis ofC. bovifaecisrevealed genes encoding anaerobic ribonucleoside triphosphate reductase (nrdDandnrdG) catalyzing the oxidation of formate to CO2while ATP is being reduced to the desoxy form. The existence ofnrdDwas verified by PCR, reverse transcription-PCR analysis and acetogenesis from formate. The process mode of acetogenesis from formate inC. bovifaecisprovides insight into the unique metabolic feature of an FDH-lacking acetogen.

IMPORTANCE

Wood-Ljungdahl pathway (WLP) lacking formate dehydrogenase (FDH) which catalyzes CO2reduction to formate has been reported to occur acetogenesis only in the presence of formate and exogenous CO2, which seems to result from the formate-rich habitats adaptation of gastrointestinal acetogens. Here, we found FDH-lackingClostridium bovifaecisstrain BXX converted formate (11.5-96 mM) into acetate with molar ratio of 2.0:1∼2.6:1 fitting the stoichiometry of acetogenesis when using formate as the sole carbon source. CO2needed in the carbonyl branch of WLP was from the oxidation of formate to CO2catalyzed by anaerobic ribonucleoside triphosphate reductase while ATP is being reduced to the desoxy form. L-cysteine in the anaerobic medium was the electron source of WLP. The process mode of acetogenesis from formate inC. bovifaecisprovides insight into how an FDH-lacking acetogen can make a living from the simplest resources as carbon source, which has both ecological and biotechnological significance.