bluuebunny/crossref_metadata_2025_split huggingface dataset:
An integrated multi-omic approach demonstrates distinct molecular signatures between human obesity with and without metabolic complications: a case–control study
Authors: Mir Fayaz Ahmad , Mall Raghvendra , Ullah Ehsan , Iskandarani Ahmad , Cyprian Farhan , Samra Tareq A. , Alkasem Meis , Abdalhakam Ibrahem , Farooq Faisal , Taheri Shahrad , Abou-Samra Abdul-Badi 
Published: March 2023

Abstract
Objectives
To examine the hypothesis that obesity complicated by the metabolic syndrome, compared to uncomplicated obesity, has distinct molecular signatures and metabolic pathways.

Methods
We analyzed a cohort of 39 participants with obesity that included 21 with metabolic syndrome, age-matched to 18 without metabolic complications. We measured in whole blood samples 754 human microRNAs (miRNAs), 704 metabolites using unbiased mass spectrometry metabolomics, and 25,682 transcripts, which include both protein coding genes (PCGs) as well as non-coding transcripts. We then identified differentially expressed miRNAs, PCGs, and metabolites and integrated them using databases such as mirDIP (mapping between miRNA-PCG network), Human Metabolome Database (mapping between metabolite-PCG network) and tools like MetaboAnalyst (mapping between metabolite-metabolic pathway network) to determine dysregulated metabolic pathways in obesity with metabolic complications.

Results
We identified 8 significantly enriched metabolic pathways comprising 8 metabolites, 25 protein coding genes and 9 microRNAs which are each differentially expressed between the subjects with obesity and those with obesity and metabolic syndrome. By performing unsupervised hierarchical clustering on the enrichment matrix of the 8 metabolic pathways, we could approximately segregate the uncomplicated obesity strata from that of obesity with metabolic syndrome.

Conclusions
The data suggest that at least 8 metabolic pathways, along with their various dysregulated elements, identified via our integrative bioinformatics pipeline, can potentially differentiate those with obesity from those with obesity and metabolic complications.
Fast and easy bioassay for the necrotizing fungus Botrytis cinerea on poplar leaves
Authors: Dreischhoff Steven , Das Ishani Shankar , Häffner Felix , Wolf Anna Malvine , Polle Andrea , Kasper Karl Henrik 
Published: March 2023

Abstract
Background
Necrotizing pathogens pose an immense economic and ecological threat to trees and forests, but the molecular analysis of these pathogens is still in its infancy because of lacking model systems. To close this gap, we developed a reliable bioassay for the widespread necrotic pathogen Botrytis cinerea on poplars (Populus sp.), which are established model organisms to study tree molecular biology.

Results
Botrytis cinerea was isolated from Populus x canescens leaves. We developed an infection system using fungal agar plugs, which are easy to handle. The method does not require costly machinery and results in very high infection success and significant fungal proliferation within four days. We successfully tested the fungal plug infection on 18 poplar species from five different sections. Emerging necroses were phenotypically and anatomically examined in Populus x canescens leaves. We adapted methods for image analyses of necrotic areas. We calibrated B. cinerea DNA against Ct-values obtained by quantitative real-time polymerase chain reaction and measured the amounts of fungal DNA in infected leaves. Increases in necrotic area and fungal DNA were strictly correlated within the first four days after inoculation. Methyl jasmonate pretreatment of poplar leaves decreased the spreading of the infection.

Conclusions
We provide a simple and rapid protocol to study the effects of a necrotizing pathogen on poplar leaves. The bioassay and fungal DNA quantification for Botrytis cinerea set the stage for in-depth molecular studies of immunity and resistance to a generalist necrotic pathogen in trees.
Childhood exposure to armed conflict and nutritional health outcomes in Nigeria
Authors: Makinde Olusesan Ayodeji , Olamijuwon Emmanuel , Mgbachi Ifeanyi , Sato Ryoko 
Published: March 2023

AbstractBackgroundArmed conflicts are associated with an increased risk of food insecurity, the leading cause of malnutrition in low-and-middle-income countries. Multiple studies have uncovered significant influences of childhood malnutrition on children’s overall health and development. As a result, it is increasingly important to understand how childhood experience of armed conflict intersects with childhood malnutrition in conflict-prone countries like Nigeria. This study examined the association between different measures of childhood experiences of armed conflicts and the nutritional health outcomes of children aged 36–59 months.MethodsWe used data from the Nigeria Demographic and Health Survey linked with Uppsala Conflict Data Program Geo-Referenced Events Dataset using geographic identifiers. Multilevel regression models were fitted on a sample of 4226 children aged 36–59 months.ResultsThe prevalence of stunting, underweight and wasting was 35%, 20% and 3%, respectively. Armed conflicts were mostly recorded in the North-eastern states of Borno (222 episodes) and Adamawa (24 episodes). Exposure to armed conflicts ranged from 0 (no experience of armed conflict) to 3.75 conflicts per month since the child’s birth. An increase in the frequency of armed conflicts is associated with increased odds of childhood stunting [AOR = 2.52, 95%CI: 1.96–3.25] and underweight [AOR = 2.33, 95%CI: 1.19–4.59] but not wasting. The intensity of armed conflict was only marginally associated with stunting and underweight but not wasting. Longer conflicts that occurred in the last year were also associated with the odds of stunting [AOR = 1.25, 95%CI: 1.17–1.33] and underweight [AOR = 1.19, 95%CI: 1.11–1.26] but not wasting.ConclusionChildhood exposure to armed conflict is associated with long-term malnutrition in children aged 36–59 months in Nigeria. Strategies that aim to end childhood malnutrition could target children exposed to armed conflicts.
Pain prevalence and pain management in children and adolescents in an italian third level pediatric hospital: a cross-sectional study
Authors: Marchetti Giuliano , Vittori Alessandro , Cascella Marco , Mascilini Ilaria , Piga Simone , Petrucci Emiliano , Castellano Aurora , Caruso Roberta , Francia Elisa , Stocchi Francesca , Marinangeli Franco , Inserra Alessandro , Picardo Sergio Giuseppe 
Published: March 2023

Abstract
Background
In 2016, we performed a one-day investigation to analyze the prevalence of pain, pain intensity, and pain therapy in the Departments of Surgery and Onco-Hematology of the Ospedale Pediatrico Bambino Gesù. To improve the knowledge gap highlighted in the previous study, refresher courses and even personalized audits have been carried out during these years. The purpose of this study is to evaluate if, after 5 years, there have been improvements in the management of pain.

Methods
The study was conducted on 25 January 2020. Pain assessment, pain therapies, pain prevalence and intensity in the preceding 24 h and during the recovery period were recorded. Pain outcomes were compared with previous audit results.

Results
Out of the 63 children with at least one documented pain assessment (starting from 100 eligible), 35 (55.4%) experienced pain: 32 children (50.7%) experienced moderate /severe pain while 3 patients (4%) felt mild pain. In the preceding 24 h, 20 patients (31.7%) reported moderate/severe pain while 10 (16%) reported moderate or severe pain during the interview. The average value of the Pain Management Index (PMI) was − 1.3 ± 0.9 with a minimum of -3 and a maximum of 0. 28 patients (87%) undergoing analgesic therapy for moderate/severe pain had a PMI of less than 0 (undertreated pain), while 3 patients (13%) scored value of 0 or higher (adequate pain therapy), 4 patients (12.5%) received multimodal analgesia with opioids and 2 patients (6%) opioids alone. Time-based therapy was prescribed to 20 patients (62.5%), intermittent therapy was prescribed to 7 patients (22%) and 5 patients (15.5%) did not receive any therapy. The prevalence of pain was higher during hospitalization and 24 h before the interview, while at the time of the interview, the proportion was the same. In this audit, the daily prescription modality of the therapy had some improvements (time-based: 62.5% vs. 44%; intermittent: 22%vs 25%; no therapy: 15.5% vs. 31%).

Conclusion
Pain management in hospitalized children constantly requires special daily attention from health professionals aimed at mitigating the components of intractable pain and resolving those of treatable pain.

Trial registration
: This study is registered with ClinicalTrials.gov, number (NCT04209764), registered 24 December 2019, https://clinicaltrials.gov/ct2/show/NCT04209764?term=NCT04209764&draw=2&rank=1.
CRISPR screens identify gene targets at breast cancer risk loci
Authors: Tuano Natasha K. , Beesley Jonathan , Manning Murray , Shi Wei , Perlaza-Jimenez Laura , Malaver-Ortega Luis F. , Paynter Jacob M. , Black Debra , Civitarese Andrew , McCue Karen , Hatzipantelis Aaron , Hillman Kristine , Kaufmann Susanne , Sivakumaran Haran , Polo Jose M. , Reddel Roger R. , Band Vimla , French Juliet D. , Edwards Stacey L. , Powell David R. , Chenevix-Trench Georgia , Rosenbluh Joseph 
Published: March 2023

AbstractBackgroundGenome-wide association studies (GWAS) have identified > 200 loci associated with breast cancer risk. The majority of candidate causal variants are in non-coding regions and likely modulate cancer risk by regulating gene expression. However, pinpointing the exact target of the association, and identifying the phenotype it mediates, is a major challenge in the interpretation and translation of GWAS.ResultsHere, we show that pooled CRISPR screens are highly effective at identifying GWAS target genes and defining the cancer phenotypes they mediate. Following CRISPR mediated gene activation or suppression, we measure proliferation in 2D, 3D, and in immune-deficient mice, as well as the effect on DNA repair. We perform 60 CRISPR screens and identify 20 genes predicted with high confidence to be GWAS targets that promote cancer by driving proliferation or modulating the DNA damage response in breast cells. We validate the regulation of a subset of these genes by breast cancer risk variants.ConclusionsWe demonstrate that phenotypic CRISPR screens can accurately pinpoint the gene target of a risk locus. In addition to defining gene targets of risk loci associated with increased breast cancer risk, we provide a platform for identifying gene targets and phenotypes mediated by risk variants.
A double-blinded, placebo-controlled, randomized study to evaluate the efficacy of perioperative dextromethorphan compared to placebo for the treatment of postoperative pain: a study protocol
Authors: Jones Ian A. , Piple Amit S. , Yan Pui Yuk , Longjohn Donald B. , Gilbert Paul K. , Lieberman Jay R. , Gucev Gligor V. , Oakes Daniel A. , Ratto Christina E. , Christ Alexander B. , Heckmann Nathanael D. 
Published: March 2023

AbstractBackgroundPain management is a critical component of comprehensive postsurgical care, as it influences patient safety and outcomes, and inadequate control has been associated with the development of chronic pain syndromes. Despite recent improvements, the management of postoperative pain following total knee arthroplasty (TKA) remains a challenge. The use of opioid-sparing, multimodal analgesic regimens has broad support, but there is a paucity of high-quality evidence regarding optimal postoperative protocols and novel approaches are needed. Dextromethorphan stands out among both well-studied and emerging pharmacological adjuncts for postoperative pain due its robust safety profile and unique pharmacology. The purpose of this study is to evaluate the efficacy of multi-dose dextromethorphan for postoperative pain control following TKA.MethodsThis is a single-center, multi-dose, randomized, double-blinded, placebo-controlled trial. A total of 160 participants will be randomized 1:1 to receive either 60 mg oral dextromethorphan hydrobromide preoperatively, as well as 30 mg 8 h and 16 h postoperatively, or matching placebo. Outcome data will be obtained at baseline, during the first 48 h, and the first two follow-up visits. The primary outcome measure will be total opioid consumption at 24 h postoperatively. Secondary outcomes related to pain, function, and quality of life will be evaluated using standard pain scales, the Knee Injury and Osteoarthritis Outcome Score for Joint Replacement (KOOS, JR) questionnaire, the Patient-Reported Outcomes Measurement Information System (PROMIS-29) questionnaire, and clinical anchors.DiscussionThis study has a number of strengths including adequate power, a randomized controlled design, and an evidence-based dosing schedule. As such, it will provide the most robust evidence to date on dextromethorphan utilization for postoperative pain control following TKA. Limitations include not obtaining serum samples for pharmacokinetic analysis and the single-center study design.Trial registrationThis trial has been registered on the National Institute of Health’sClinicalTrials.gov(NCT number: NCT05278494). Registered on March 14, 2022.
Making a voice heard: evaluation of a new service delivery in augmentative and alternative communication through qualitative interviews with people without natural speech
Authors: Zinkevich Anna , Uthoff Sarah Anna Katharina , Boenisch Jens , Sachse Stefanie Kalén , Schnack Helge , Garbe Carolin , Bernasconi Tobias , Ansmann Lena 
Published: March 2023

Abstract
Objective
Due to communication barriers, people without natural speech who use augmentative and alternative communication (AAC) are rarely interviewed about their healthcare needs, expectations, and experiences. This qualitative interview study aims to investigate how AAC users evaluate a new service delivery (nSD) in AAC care in Germany.

Results
We conducted 8 semi-structured qualitative interviews with 8 AAC users. The results of the performed qualitative content analysis show a positive evaluation of the nSD among AAC users. Contextual factors were identified that seem to hinder the achievement of the intervention goals. These include caregivers' prejudice and inexperience with AAC and an unfavourable environment in which AAC is used.
Existence of positive solutions for Lidstone boundary value problems on time scales
Authors: Çetin Erbil , Topal Fatma Serap , Agarwal Ravi P. 
Published: March 2023

AbstractLet$\mathbb{T}\subseteq \mathbb{R}$T⊆Rbe a time scale. The purpose of this paper is to present sufficient conditions for the existence of multiple positive solutions of the following Lidstone boundary value problem on time scales:$$\begin{aligned} &(-1)^{n} y^{\Delta ^{(2n)}}(t) = f\bigl(t, y(t)\bigr), \quad \text{$t\in [a,b]_{ \mathbb{T}}$,} \\ &y^{\Delta ^{(2i)}}(a)= y^{\Delta ^{(2i)}}\bigl(\sigma ^{2n-2i}(b)\bigr)=0,\quad i=0,1,\ldots,n-1. \end{aligned}$$(−1)nyΔ(2n)(t)=f(t,y(t)),t∈[a,b]T,yΔ(2i)(a)=yΔ(2i)(σ2n−2i(b))=0,i=0,1,…,n−1.Existence of multiple positive solutions is established using fixed point methods. At the end some examples are also given to illustrate our results.
Implementation of community-based management of severe acute malnutrition in conflict affected regions: a case of South Kordofan, Sudan
Authors: Sserwanja Quraish , Adam Osman Omer , Mohamed Eissa Hassan , Adam Mohammed Bashir , Mutisya Linet M. 
Published: March 2023

AbstractMalnutrition is the major cause of mortality and morbidity globally with undernutrition contributing about 45% of all deaths of under five children. Besides the direct effects of protracted conflicts, the macroeconomic crisis that has greatly increased the national inflation rate hence devastating the purchasing power, the COVID-19 outbreak, flooding, and the Desert Locusts have contributed to a food security emergency. Besides being among the most under resourced states, South Kordofan has experienced years of conflict resulting in displacement of people and extensive infrastructure destruction with high rates of malnutrition. The state currently has 230 health facilities and out of these, only 140 are providing outpatient therapeutic programme centres with 28.6% (40) of these being operated by the state ministry of health and the rest by the international non-governmental organizations. Limited resources leading to donor dependence, limited accessibility due to insecurity and floods, poor referral system and gaps in continuity of care, lack of operational and implementation research data and limited integration of management of malnutrition in other health services have negatively affected effective implementation. Ensuring effective and efficient community based management of acute malnutrition, implementation needs action beyond the health sector with a multi-sectoral and integration approach. Federal and state development frameworks should ensure a comprehensive multi-sectoral nutrition policy with strong political commitment and allocation of adequate resources to ensure integrated and quality implementation.
Modelling human lower urinary tract malformations in zebrafish
Authors: Kolvenbach Caroline M. , Dworschak Gabriel C. , Rieke Johanna M. , Woolf Adrian S. , Reutter Heiko , Odermatt Benjamin , Hilger Alina C. 
Published: March 2023

AbstractAdvances in molecular biology are improving our understanding of the genetic causes underlying human congenital lower urinary tract (i.e., bladder and urethral) malformations. This has recently led to the identification of the first disease-causing variants in the gene BNC2 for isolated lower urinary tract anatomical obstruction (LUTO), and of WNT3 and SLC20A1 as genes implicated in the pathogenesis of the group of conditions called bladder-exstrophy-epispadias complex (BEEC). Implicating candidate genes from human genetic data requires evidence of their influence on lower urinary tract development and evidence of the found genetic variants’ pathogenicity. The zebrafish (Danio rerio) has many advantages for use as a vertebrate model organism for the lower urinary tract. Rapid reproduction with numerous offspring, comparable anatomical kidney and lower urinary tract homology, and easy genetic manipulability by Morpholino®-based knockdown or CRISPR/Cas editing are among its advantages. In addition, established marker staining for well-known molecules involved in urinary tract development using whole-mount in situ hybridization (WISH) and the usage of transgenic lines expressing fluorescent protein under a tissue-specific promoter allow easy visualization of phenotypic abnormalities of genetically modified zebrafish. Assays to examine the functionality of the excretory organs can also be modeled in vivo with the zebrafish. The approach of using these multiple techniques in zebrafish not only enables rapid and efficient investigation of candidate genes for lower urinary tract malformations derived from human data, but also cautiously allows transferability of causality from a non-mammalian vertebrate to humans.
Peritoneal dialysis-related peritonitis with encapsulated ascites due to Mycobacterium abscessus subsp. massilience and subsp. bolletii: a case series and literature review
Authors: Nagasaka Tomoki , Uchiyama Kiyotaka , Shirai Ryoichi , Mitsuno Ryunosuke , Maruki Tomomi , Hama Eriko Yoshida , Sugita Erina , Kusahana Ei , Sumura Rena , Nakayama Takashin , Kinugasa Satoshi , Morimoto Kohkichi , Ishibashi Yoshitaka , Washida Naoki , Itoh Hiroshi 
Published: March 2023

Abstract
Background
As there is no established standard of care for non-tuberculous mycobacterium (NTM) peritoneal dialysis (PD)-related peritonitis, its treatments have to be case-dependent, which is often difficult. Additionally, several reported cases were accompanied by encapsulated ascites, adhesive ileus, and encapsulating peritoneal sclerosis, suggesting treatment difficulties. We report two cases of PD-related peritonitis with encapsulated ascites due to Mycobacterium abscessus subsp. massilience and subsp. bolletii. To the best of our knowledge, this is the first case series to report PD-related peritonitis caused by Mycobacterium abscessus subsp. bolletii.

Case presentation
The first case is that of a 74-year-old male patient who started PD six years ago for end-stage renal failure due to diabetic nephropathy. In February 2021, he presented with signs of infection at the exit-site and swelling of the tunnel. Mycobacterium abscessus subsp. massilience was detected in the culture of the exit-site exudate; thus, he was diagnosed with tunnel infection (caused by NTM). Subsequently, fever, abdominal pain, and increased cell counts in the PD drainage fluid were observed, and he was judged to have NTM peritonitis. His general condition improved after PD catheter removal in addition to antimicrobial treatment and encapsulated ascites drainage. The second case is that of a 52-year-old man who commenced PD for end-stage renal failure due to nephrosclerosis 12 years ago. In May 2022, he was diagnosed with PD-related peritonitis based on signs of infection at the exit-site, encapsulated ascites on computed tomography, and a cloudy PD drainage fluid. Mycobacterium abscessus subsp. bolletii was detected in the culture of the exit-site exudate, which led to the diagnosis of NTM peritonitis. In addition to antimicrobial treatment, PD catheter removal and encapsulated ascites drainage were performed. The patient also had adhesive bowel obstruction due to peritonitis and required decompression therapy with the insertion of a gastric tube.

Conclusions
PD catheter removal and encapsulated ascites drainage might have improved inflammation and treatment outcomes. Additionally, Mycobacterium abscessus might be prone to forming encapsulated cavities and/or intestinal adhesions; however, further accumulation of cases clarifying “subspecies” of Mycobacterium abscessus is necessary to confirm this hypothesis.
Cortical deafness as a sequel of recurrent stroke in patient with prosthetic heart valves and atrial fibrillation: a case report
Authors: Rasyid Al , Mesiano Taufik , Kurniawan Mohammad , Hidayat Rakhmad , Prawiroharjo Pukovisa , Pudianto Angga Pramudita , Jundi Achmad Faisal , Wiyarta Elvan , Harris Salim 
Published: March 2023

Abstract
Background
Cortical deafness is an unusual occurrence caused by injury to the central auditory pathway but not to the hearing organ. This paper reports the first case of cortical deafness as a sequel of recurrent stroke in a patient with prosthetic heart valves and atrial fibrillation in Asia.

Case presentation
A 40-year-old man with a history of atrial fibrillation and valvular heart disease comes with weakness on the right side of the body and slurred speech. Examination showed hemiplegia with increased d-dimer and activated partial thromboplastin time. (APTT). Brain MRI showed multiple subacute infarctions in the temporal lobe. Diffusion Tensor Imaging (DTI) tractography showed no visible auditory tract. Pure tone audiogram and brainstem auditory evoked potential test was normal, but speech reception threshold test was very poor. The patient has been diagnosed with recurrent ischemic stroke with sequel cortical deafness and received anticoagulant therapy and speech therapy. The patient reported minimal subjective impairment 1 month later with no further neurological deterioration.

Conclusions
A multidisciplinary clinical approach is needed in patients with cortical deafness, especially distinguishing it from other central hearing losses.