bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prospective, multicenter study of antimicrobial-coated, noncrosslinked, acellular porcine dermal matrix (XenMatrix™ AB Surgical Graft) for hernia repair in all centers for disease control and prevention wound classes: 24-month follow-up cohort
Authors: IIahi Obeid N. , Velmahos George , Janis Jeffrey E. , Kovach Stephen J. , McLean Susan F. , Askari Reza , Sommer Courtney A. , Agarwal Suresh , Srinivasan Jahnavi , Wong Alex K. , Pakula Andrea , Miranda Edward P. , Breen Kerry , Shapiro Mark , Deeken Corey R. , Stringer R. Cody , McGraw J. Reed , Bascone Corey , Martindale Robert G. 
Published: March 2024

Background:
Prospective, multicenter, single-arm study of antimicrobial-coated, noncrosslinked, acellular porcine dermal matrix (AC-PDM) in a cohort involving all centers for disease control and prevention wound classes in ventral/incisional midline hernia repair (VIHR).

Materials and methods:
Seventy-five patients (mean age 58.6±12.7 years; BMI 31.3±4.9 kg/m2) underwent ventral/incisional midline hernia repair with AC-PDM. Surgical site occurrence (SSO) was assessed in the first 45 days post-implantation. Length of stay, return to work, hernia recurrence, reoperation, quality of life, and SSO were assessed at 1, 3, 6, 12, 18, and 24 months.

Results:
14.7% of patients experienced SSO requiring intervention within 45 days post-implantation, and 20.0% thereafter (>45 d post-implantation). Recurrence (5.8%), definitely device-related adverse events (4.0%), and reoperation (10.7%) were low at 24 months; all quality-of-life indicators were significantly improved compared to baseline.

Conclusion:
AC-PDM exhibited favourable results, including infrequent hernia recurrence and definitely device-related adverse events, with reoperation and SSO comparable to other studies, and significantly improved quality of life.
Conservative therapy of severe acute pancreatitis is a safe option – results of a 15-year long-term follow-up cohort study
Authors: Alsfasser Guido , Klar Ernst , Feitl Judith , Schafmayer Clemens 
Published: March 2024

Background:
Treatment of severe acute pancreatitis can be challenging with high mortality. In 2012 we reported a significantly reduced in-hospital mortality if these patients are treated conservatively for at least the first 3 weeks in the course of the disease as compared to early necrosectomy. We performed a long-term follow-up and compared the outcome of these two study groups (group 1 – early necrosectomy, n=20 versus group 2 – primary conservative treatment, n=24).

Materials and methods:
Follow-up of the study patients by personal contact, phone survey, or data from primary care physician. Median follow-up was 15 years (range 10–22 years). This trial is registered at: Research Registry UIN researchregistry8697.

Results:
Eleven survivors of group 1 and 22 survivors of group 2 were discharged after initial treatment. Ten of 11 surviving patients of group 1 (90.9%) and 20 of 22 surviving patients of group 2 (90.9%) were included in this study. Between groups, there were no statistical differences in the rate of resubmission (P=0.23), development of diabetes (P=0.78), or development of exocrine insufficiency (P=1.0). However, long-term survival in group 2 was significantly better than that of group 1 (P=0.049).

Conclusion:
Primary conservative treatment of severe acute pancreatitis without early necrosectomy does not lead to early complications and even shows an advantage in long-term survival. Therefore conservative treatment of severe acute pancreatitis is safe and there is no absolute need for necrosectomy in severe acute pancreatitis.
Accuracy prediction of Goodsall’s rule for anal fistulas of crypotogladular origin, is still standing?
Authors: Bakir Qais Khadim , Noori Ibrahim Falih , Noori Ahmed Falih 
Published: March 2024

Background:
Treatment of anal fistulas is still a challenging task because of high recurrence and risk of incontinence. Identification of internal fistula opening is paramount for successful treatment. Goodsall’s rule is commonly used to predict the course of fistula and internal opening. However, its accuracy has been questioned by many investigators and its role became a controversial topic.

Method:
This is a case series prospective study in which 320 consecutive patients with anal fistula with Mean age 48.9± 6 years ages (ranges from 16 to 64 years) and mean body mass index 24.8± 5.5 average 18.5–30.6) were enroled. Goodsall’s rule was applied to all fistulas according to the site of external fistula opening. Location of internal fistula opening as suggested by Goodsall’s rule then compared to the exact location of internal opening identified by perineal or pelvic MRI and intraoperative findings. to assess the accuracy and positive predictive value of the Goodsall’s rule in predicting the internal opening of the tract.

Results:
The overall accuracy rate, positive predictive value (PPV), sensitivity and specificity of Goodsall’s rule in this study were 74.75%, 77.1, 74.5, and 72.05, respectively. The accuracy in predicting the internal fistula opening was 52.4% in anterior tracts and 73% in posterior tracts. Goodsall’s rule was found to be more accurate in posterior fistulas than anterior fistulas and in short superficial fistulas rather than in long and high fistulas.

Conclusion:
Goodsall’s rule was accurate in 74.75% of anal fistulas. It was more accurate for posterior long fistulas and anterior short and superficial fistulas. Patients with long (>3 cm) anterior fistulas defied Goodsall’s rule when they found to have fistulas tracking to a midline anterior origin. Further, short posterior fistulas were found to open more commonly in a direct radial course rather to midline posteriorly.
Medical malpractice and epidural hematomas: a retrospective analysis of 101 cases in the United States
Authors: Pecorari Isabella L. , Agarwal Vijay 
Published: March 2024

Background:
Neurosurgeons face particularly high rates of litigation compared to physicians in other fields. Malpractice claims are commonly seen after mismanagement of life-threatening medical emergencies, such as epidural hematomas. Due to the lack of legal analysis pertaining to this condition, the aim of this study is to identify risk factors associated with litigation in cases relating to the diagnosis and treatment of epidural hematomas.

Materials and Methods:
Westlaw Edge, an online database, was used to analyze malpractice cases related to epidural hematomas between 1986 to 2022. Information regarding plaintiff demographics, defendant specialty, reason for litigation, trial outcomes, and payouts for verdicts and settlements were recorded. Comparative analysis between cases that returned a jury verdict in favor of the plaintiff versus defendant was completed.

Results:
A total of 101 cases were included in the analysis. Failure to diagnose was the most common reason for litigation (n = 64, 63.4%), followed by negligent care resulting in an epidural hematoma (n = 44, 43.6%). Spine surgery (n = 29, 28.7%), trauma (n = 28, 27.7%), and epidural injection/catheter/electrode placement (n = 21, 20.8%) were the primary causes of hematomas. Neurosurgeons (n = 18, 17.8%) and anesthesiologists (n = 17, 16.8%) were the two most common physician specialties cited as defendants. Most cases resulted in a jury verdict in favor of the defense (n = 54, 53.5%). For cases ending in plaintiff verdicts, the average payout was $3,621,590.45, while the average payment for settlements was $2,432,272.73.

Conclusion:
Failure to diagnose epidural hematomas is the most common reason for malpractice litigation, with neurosurgeons and anesthesiologists being the most common physician specialties to be named as defendants. More than half of all cases returned a jury verdict in favor of the defense and, on average, settlements proved to be more cost-effective than plaintiff verdicts.
Knowledge, attitudes, and perceptions of physical therapists towards conventional physical therapy-across-sectional study
Authors: Albishi Alaa. M. 
Published: March 2024

Background:
Conventional physical therapy (CPT) is widely used in clinical practice and known to contribute beneficially to patient’s health conditions but remains loosely defined. Research has shown inconsistency in the definition and utilization of CPT among physical therapists in clinical and research settings, limiting its generalisability and reproducibility. Therefore, this study evaluates physical therapists’ knowledge, attitudes, and perceptions toward CPT.

Methods:
A cross-sectional study using a self-administered questionnaire containing 36 questions was distributed among 238 licensed physical therapists. Descriptive and inferential statistics were used to measure the physical therapists’ knowledge, attitudes, and perceptions towards CPT.

Results:
Physical therapists showed limited knowledge of CPT in rehabilitation (4.09±1.698, 51%). However, the knowledge scores were significantly associated with age (P=0.002), educational levels (P=0.006), and years of work experience (P=0.001). Nevertheless, physical therapists showed an overall positive attitude towards CPT and perceived it as essential to rehabilitation.

Conclusion:
Most physical therapists have low knowledge about CPT but positive attitudes and perceptions. Therefore, customized medical education is necessary to incorporate CPT theories and applications into physical therapists’ rehabilitation programs.
Nationwide Longitudinal Annual Survey of HIV/AIDS Referral Hospitals in Japan From 1999 to 2021: Trend in Non–AIDS-defining Cancers Among Individuals Infected With HIV-1
Authors: Tanaka Takeshi , Oshima Kazuhiro , Kawano Kei , Tashiro Masato , Kakiuchi Satoshi , Tanaka Akitaka , Fujita Ayumi , Ashizawa Nobuyuki , Tsukamoto Misuzu , Yasuoka Akira , Teruya Katsuji , Izumikawa Koichi 
Published: March 2024

Background:
Non–AIDS-defining cancers (NADCs) in patients infected with HIV have recently attracted attention because of the improved survival of this patient population. To obtain accurate data, a longitudinal study is warranted for the nationwide surveillance of the current status and national trend of NADCs in patients infected with HIV in Japan.

Setting:
An annual nationwide surveillance of NADCs in patients infected with HIV-1 in Japan from 1999 to 2021.

Methods:
An annual questionnaire was sent to 378 HIV/AIDS referral hospitals across Japan to collect data (clusters of differentiation 4-positive lymphocytes, time of onset, outcomes, and antiretroviral therapy status) of patients diagnosed with any of the NADCs between 1999 and 2021.

Results:
The response and case-capture rates for the questionnaires in 2021 were 37.8% and 81.2%, respectively. The number of reported NADC cases subsequently increased since the beginning of this study. Evaluation of the case counts of NADCs demonstrated a high incidence of lung, colorectal, gastric, and liver cancers as the top 4 cancers. Pancreatic cancer (0.63), lung cancer (0.49), and leukemia (0.49) had the highest mortality rates among the NADCs. Trends of NADCs regarding transmission routes were maintained over the years in male individuals who have sex with male individuals compared with heterosexual male individuals and female individuals.

Conclusions:
We demonstrated an increasing trend in the incidence of NADCs over a period of 23 years in Japan. The current data highlighted the importance of raising awareness regarding cancer management for patients infected with HIV in Japan.
NAD+activates renal metabolism and protects from chronic kidney disease in a model of Alport syndrome
Authors: Jones Bryce A. , Gisch Debora L. , Myakala Komuraiah , Sadiq Amber , Cheng Ying-Hua , Taranenko Elizaveta , Panov Julia , Korolowicz Kyle , Melo Ferreira Ricardo , Yang Xiaoping , Santo Briana A. , Allen Katherine C. , Yoshida Teruhiko , Wang Xiaoxin X. , Rosenberg Avi Z. , Jain Sanjay , Eadon Michael T. , Levi Moshe 
Published: March 2024

ABSTRACTChronic kidney disease (CKD) is associated with renal metabolic disturbances, including impaired fatty acid oxidation (FAO). Nicotinamide adenine dinucleotide (NAD+) is a small molecule that participates in hundreds of metabolism-related reactions. NAD+levels are decreased in CKD, and NAD+supplementation is protective. However, both the mechanism of how NAD+supplementation protects from CKD, as well as the cell types involved, are poorly understood. Using a mouse model of Alport syndrome, we show that nicotinamide riboside (NR), an NAD+precursor, stimulates renal peroxisome proliferator-activated receptor alpha signaling and restores FAO in the proximal tubules, thereby protecting from CKD in both sexes. Bulk RNA-sequencing shows that renal metabolic pathways are impaired in Alport mice and activated by NR in both sexes. These transcriptional changes are confirmed by orthogonal imaging techniques and biochemical assays. Single nuclei RNA-sequencing and spatial transcriptomics, both the first of their kind from Alport mice, show that NAD+supplementation restores FAO in proximal tubule cells. Finally, we also report, for the first time, sex differences at the transcriptional level in this Alport model. In summary, we identify a nephroprotective mechanism of NAD+supplementation in CKD, and we demonstrate that the proximal tubule cells substantially contribute to this benefit.
Exploring Genomic Large Language Models: Bridging the Gap between Natural Language and Gene Sequences
Authors: Liu Huaqing , Zhou Shuxian , Chen Peiyi , Liu Jiahui , Huo Ku-Geng , Han Lanqing 
Published: March 2024

AbstractMotivationWith the rapid development of genomic sequencing technologies and accumulation of sequencing data, there is an increasing demand for analysis tools that are more user-friendly for non-programmer users. In support of this initiative, we developed an all-in-one tool called GenomicLLM that can understand simple grammar in the question input and perform different types of analyses and tasks accordingly.ReaultsWe trained the GenomicLLM model using three large open-access datasets, namely GenomicLLM_GRCh38, Genome Understanding Evaluation and GenomicBenchmarks, and developed a hybrid tokenization approach to allow better comprehension from mixed corpora that include sequence and non-sequence inputs. GenomicLLM can carry out a wider range of tasks. In the classification tasks that are also available in the state-of-the-art DNABERT-2 and HyenaDNA, GenomicLLM has comparable performance. Moreover, GenomicLLM can also carry out other regression and generation tasks that are not accomplishable by these tools. In summary, we demonstrated here a successful large language model with a mixture of gene sequences and natural language corpus that enables a wider range of applications.Availability and implementationCodes and data can be accessed athttps://github.com/Huatsing-Lau/GenomicLLMandhttps://zenodo.org/records/10695802
Separation of telomere protection from length regulation by two different point mutations at amino acid 492 of RTEL1
Authors: Smoom Riham , May Catherine Lee , Lichtental Dan , Skordalakes Emmanuel , Kaestner Klaus H. , Tzfati Yehuda 
Published: March 2024

AbstractRTEL1 is an essential DNA helicase that plays multiple roles in genome stability and telomere length regulation. A variant of RTEL1 with a lysine at position 492 is associated with short telomeres inMus spretus, while a conserved methionine at this position is found inM. musculus, which has ultra-long telomeres. In humans, a missense mutation at this position (Rtel1M492I) causes a fatal telomere biology disease termed Hoyeraal-Hreidarsson syndrome (HHS). Introducing theRtel1M492Kmutation intoM. musculusshortened the telomeres of the resulting strain, termed ‘Telomouse’, to the length of human telomeres. Here, we report on a mouse strain carrying theRtel1M492Imutation, termed ‘HHS mouse’. The HHS mouse telomeres are not as short as those of Telomice but nevertheless they display higher levels of telomeric DNA damage, fragility and recombination, associated with anaphase bridges and micronuclei. These observations indicate that the two mutations separate critical functions of RTEL1: M492K mainly reduces the telomere length setpoint, while M492I predominantly disrupts telomere protection. The two mouse models enable dissecting the mechanistic roles of RTEL1 and the different contributions of short telomeres and DNA damage to telomere biology diseases, genomic instability, cancer, and aging.
Device Design and Diagnostic Imaging of Radiopaque 3D Printed Tissue Engineering Scaffolds
Authors: Delemeester Mitchell , Pawelec Kendell M. , Hix Jeremy M.L. , Siegenthaler James R. , Lissy Micah , Douek Philippe , Houmeau Angèle , Si-Mohamed Salim , Shapiro Erik M. 
Published: March 2024

ABSTRACT3D printed biomaterial implants are revolutionizing personalized medicine for tissue repair, especially in orthopedics. In this study, a radiopaque Bi2O3doped polycaprolactone (PCL) composite is developed and implemented to enable the use of diagnostic X-ray technologies, especially photon counting X-ray computed tomography (PCCT), for comprehensive in vivo device monitoring. PCL filament with homogeneous Bi2O3nanoparticle (NP) dispersion (0.8 to 11.7 wt%) are first fabricated. Tissue engineered scaffolds (TES) are then 3D printed with the composite filament, optimizing printing parameters for small feature size and severely overhung geometries. These composite TES are characterized via micro-computed tomography (µCT), tensile testing, and a cytocompatibility study, with Bi2O3mass fractions as low as 2 wt% providing excellent radiographic distinguishability, improved tensile properties, and equivalent cytocompatibility of neat PCL. The excellent radiographic distinguishability is validated in situ by imaging 4 and 7 wt% TES in a mouse model with µCT, showing excellent agreement with in vitro measurements. Subsequently, CT image-derived swine menisci are 3D printed with composite filament and re-implanted in their corresponding swine legsex vivo. Re-imaging the swine legs via clinical CT allows facile identification of device location and alignment. Finally, the emergent technology of PCCT unambiguously distinguishes implanted menisci in situ.
Azadirachta indica:derived, red-emitting, carbon nanoparticles for cellular bioimaging and potential therapeutics
Authors: Gandhi Stuti , Jain Sweny , Bhatia Dhiraj , Yadav Pankaj 
Published: March 2024

AbstractRed-emitting carbon nanoparticles (CNPs) were synthesized by the refluxed green synthesis method using ethanolic extract of neem leaves (Azadirachta indica). These nanoparticles were called as nQDs (neem quantum dots). The nQDs exhibited excellent photoluminescence properties with a maximum emission at 672nm, and the average size of nQDs was around 47nm. In thein-vitrostudy, Retinal Pigment epithelial (RPE1) cells and SUM159A cells showed enhanced cellular uptake. In RPE1 cells, the cellular uptake was higher than in SUM159A cells. In the biocompatibility assay, SUM159A cell viability declined with the increasing nQDs concentration. The results show that red-emissive CNPs can be synthesized fromAzadirachta indica(neem) leaves using a simple method with a possible application in bioimaging and therapeutics.Abstract Figure
Oolonghomobisflavans fromCamellia sinensisdisaggregate tau fibrils across Alzheimer’s disease models
Authors: Duangjan Chatrawee , Chang Xinmin , Seidler Paul M. , Curran Sean P. 
Published: March 2024

ABSTRACTAlzheimer’s disease (AD) is a common debilitating neurodegenerative disease with limited treatment options. Amyloid-β (Aβ) and tau fibrils are well-established hallmarks of AD, which can induce oxidative stress, neuronal cell death, and are linked to disease pathology. Here, we describe the effects of Oolonghomobisflavan A (OFA) and Oolonghomobisflavan B (OFB) on tau fibril disaggregation and prionogenic seeding. Transcriptomic analysis of OF-treated animals reveals the induction of a proteostasis-enhancing and health-promoting signature. OFA treatment reduced the burden of Tau protein aggregation in aC. elegansmodel expressing pathogenic human tau (“hTau-expressing”) and promoted Tau disaggregation and inhibited seeding in assays usingex vivobrain-derived paired helical filament tau protein fibrils from Alzheimer’s disease brain donors. Correspondingly, treatment with OF improved multiple fitness and aging-related health parameters in the hTau-expressingC. elegansmodel, including reproductive output, muscle function, and importantly, reversed the shortened lifespan stemming from pathogenic Tau expression. Collectively, this study provides new evidence supporting the neuroprotective effects of OFs and reveal a new therapeutic strategy for targeting AD and other neurodegenerative diseases characterized by tauopathy.
A temporal sequence of heterochronic gene activities promotes stage-specific developmental events inC. elegans
Authors: Ivanova Maria , Moss Eric G. 
Published: March 2024

AbstractThe heterochronic genes of the nematodeCaenorhabditis eleganscontrol the succession of postembryonic developmental events. The four core heterochronic geneslin-14, lin-28, hbl-1,andlin-41act in a sequence to specify cell fates specific to each of the four larval stages. It was previously shown thatlin-14has two activities separated in time that promote L1 and L2 developmental events, respectively. Using the auxin-inducible degron system, we find thatlin-28andhbl-1each have two activities that control L2 and L3 events which are also separated in time. Relative to events they control, bothlin-28andhbl-1appear to act just prior to or concurrently with events of the L2. Relative to each other,lin-28andhbl-1appear to act simultaneously. By contrast, thelin-14activity controlling L2 events precedes those oflin-28andhbl-1controlling the same events, suggestinglin-14’s regulation oflin-28is responsible for the delay. Likewise, the activities oflin-28andhbl-1controlling L3 fates act well in advance of those fates, suggesting a similar regulatory gap.lin-41acts early in the L3 to affect fates of the L4, although it was not possible to determine whether it too has two temporally separated activities. We also uncovered a feedback phenomenon that prevents the reactivation of heterochronic gene activity late in development after it has been down-regulated. This study places the heterochronic gene activities into a timeline of postembryonic development relative to one another and to the developmental events whose timing they control.