bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is Ophthalmia Neonatorum Associated With Invasive Bacterial Infection? A Single-Center Retrospective Study
Authors: St-Onge-St-Hilaire Alexandra , Boutin Ariane , Gravel Jocelyn 
Published: October 2023

ObjectiveOphthalmia neonatorum (ON) is a conjunctivitis occurring in neonates and can be caused by multiple bacterial pathogens. The risk of invasive bacterial infection (IBI) in neonates with ON is poorly known. Our objectives were to document the association of ON with IBI in term neonates and to investigate practice variation.MethodsThis was a retrospective observational study of all neonates who presented to a single emergency department (ED) between January 2018 and December 2019. Participants were all children with a final diagnosis of ON according to the treating physician as registered in the ED computerized database. Newborns with craniofacial malformations and premature infants were excluded. The primary outcome was IBI as defined by growth of any bacterial pathogen in the blood or cerebrospinal fluid. Perinatal risk factors, ED visit details (symptoms on presentation, management, and treatment plan) as well as complications (ocular morbidity, death, and unscheduled return visits) were collected. Data were analyzed using descriptive statistics.ResultsFifty-two term neonates were included. There were no cases of IBI associated with ON (0%; 95% confidence interval [CI], 0%–6.9%). Six ocular bacterial infections were identified, one of which wasChlamydia trachomatis. Although there were no IBIs, ocular complications, deaths, or unscheduled return visits to the ED, there was a wide variation in physician's management of ON. Physicians ordered investigations in 49% (95% CI, 34%–62%) of neonates, prescribed antibiotics to 87% (95% CI, 74%–94%), and involved specialists in 39% (95% CI, 27%–52%) of cases.ConclusionsEmergency department presentations of term neonates with ON are associated with a low risk of IBI. A better understanding of the current practice variation is needed to inform clinical guidelines for the management of neonates with ON presenting to the ED.
Ready, Set, Move! Tracking Children's Modified Ride-On Car Use With a Custom Data Logger
Authors: Dean-Hergert Sarah M. , Papazian Christina , Barchus Rebecca , Barroero Chelsea , Schnare Wendy , Logan Samuel W. , Feldner Heather A. , Winfree Kyle N. 
Published: October 2023

Purpose:
To create and implement a next-generation, custom data logger to automatically track modified ride-on car (MROC) use in home and community settings, establish feasibility of long-term remote collection of community MROC use data, describe trends of MROC use, and explore parent perception of the MROC.

Methods:
In this descriptive study, a custom data logger was constructed and integrated into MROCs using an Arduino Pro-Mini microprocessor to capture real-time use data remotely.

Results:
It is feasible to automatically track MROC use in home and community settings. On average, MROC use trends appear consistent with caregiver reports and show higher initial use with steadily decreasing frequency over time, and varying bout duration and play session length, despite favorable caregiver perceptions of the cars.

Conclusions:
Remote tracking of MROC use may decrease burden on busy families and provide clinicians with valuable technology use data.
Management strategies for severe Pseudomonas aeruginosa infections
Authors: Do Rego Hermann , Timsit Jean-François 
Published: October 2023

Purpose of review
This review focuses on the management of severe Pseudomonas aeruginosa infections in critically ill patients.

Recent findings

Pseudomonas aeruginosa is the most common pathogen in intensive care; the main related infections are nosocomial pneumonias, then bloodstream infections. Antimicrobial resistance is common; despite new antibiotics, it is associated with increased mortality, and can lead to a therapeutic deadlock.

Summary
Carbapenem resistance in difficult-to-treat P. aeruginosa (DTR-PA) strains is primarily mediated by loss or reduction of the OprD porin, overexpression of the cephalosporinase AmpC, and/or overexpression of efflux pumps. However, the role of carbapenemases, particularly metallo-β-lactamases, has become more important. Ceftolozane-tazobactam, ceftazidime-avibactam and imipenem-relebactam are useful against DTR phenotypes (noncarbapenemase producers). Other new agents, such as aztreonam-ceftazidime-avibactam or cefiderocol, or colistin, might be effective for carbapenemase producers. Regarding nonantibiotic agents, only phages might be considered, pending further clinical trials. Combination therapy does not reduce mortality, but may be necessary for empirical treatment. Short-term treatment of severe P. aeruginosa infections should be preferred when it is expected that the clinical situation resolves rapidly.
Uptake of Gadolinium-Based Contrast Agents by Blood Cells During Contrast-Enhanced MRI Examination
Authors: Ruprecht Nico , Parakkattel Dixy , Hofmann Lukas , Broekmann Peter , Lüdi Nicola , Kempf Christoph , Heverhagen Johannes Thomas , von Tengg-Kobligk Hendrik 
Published: October 2023

ObjectivesGadolinium-based contrast agents (GBCAs) are routinely used in magnetic resonance imaging (MRI) examinations. However, there is limited knowledge about the interaction with and distribution of the drug in human cells. This lack of knowledge is surprising, given that the first interaction of the drug occurs with blood cells. Moreover, recent studies reported gadolinium (Gd) deposition within organs, such as the brain. Hence, this study is aiming to determine the uptake of GBCA in blood cells of patients undergoing contrast-enhanced MRI (ce-MRI) examination.Materials and MethodsHuman blood was exposed to either gadoterate meglumine (Gd-DOTA) or Eu-DOTA in vitro or was collected from patients undergoing ce-MRI with Gd-DOTA. Uptake of contrast agents (CAs) by blood cells was quantified by Gd measurements using single-cell inductively coupled plasma mass spectrometry (SC-ICP-MS) or, to confirm Gd-DOTA uptake, by a complementary method using Eu-DOTA by time-resolved fluorescence spectroscopy, respectively.ResultsUptake of Gd-DOTA or Eu-DOTA into white blood cells (WBCs) ex vivo was detectable by SC-ICP-MS and time-resolved fluorescence spectroscopy. The intracellular concentrations were estimated to be in the range of 1–3 μM. However, no CA uptake into erythrocytes was detected with either method. In total, 42 patients between 30 and 84 years old (24 men, 18 women) were enrolled. White blood cells' uptake of Gd was measured by SC-ICP-MS. Isolated WBCs from patients who underwent ce-MRI examination showed substantial Gd uptake; however, the studied patient group showed an inhomogeneous distribution of Gd uptake. Measurements immediately after MRI examination indicated 21–444 attogram/WBC, corresponding to an intracellular Gd concentration in the range from 0.2 to 5.5 μM.ConclusionsThis study confirms the ex vivo uptake of GBCA by WBCs and provides the first evidence that GBCA is indeed taken up by WBCs in vivo by patients undergoing ce-MRI examination. However, the observed Gd uptake in WBCs does not follow a log-normal distribution commonly observed in the fields of environmental studies, biology, and medicine. Whether cellular uptake of GBCA is linked to the observed deposition of Gd remains unclear. Therefore, studying the interaction between GBCA and human cells may clarify crucial questions about the effects of Gd on patients after MRI examinations.
Successful Reconstruction of Complex Sacrococcygeal Defects Using Chimeric Perforator Propeller Flap
Authors: Yu Zouzou , Jin Shengyang , Zang Mengqing , Zhu Shan , Li Shanshan , Han Tinglu , Chen Zixiang , Liu Yuanbo 
Published: October 2023

Background
Complex soft tissue defects, which result from the surgical resection of sacral tumors, manifest as a combination of skin defects, dead space, infection, and prosthesis exposure. Because the traditional musculocutaneous flap lacks flexibility because of the close connection between the skin flap and the muscle component, the musculocutaneous flap is not suitable for reconstructing complex soft tissue defects where the dead space and skin defects are located at different sites. Furthermore, the perforator flap is also not appropriate for reconstructing complex defects because it lacks the muscular component. We considered the possibility of using the chimeric perforator propeller flap for reconstructing complex sacrococcygeal defects.

Methods
This study included 7 patients who underwent, between July 2007 and July 2021, the reconstruction of complex soft tissue defects of the sacrococcygeal region using a chimeric perforator propeller flap.

Results
Among the included cases, the etiologies were chordoma (n = 3), sacral tumor (n = 3), and squamous cell carcinoma (n = 1). In all the cases, vacuum-assisted closure therapy was used to treat wound infections before surgery. The average sizes of the skin and muscle flaps were 195.8 cm2 (range, 100–350 cm2) and 83.6 cm2 (range, 60–140 cm2), respectively. The superior gluteal artery was the source artery for the chimeric perforator propeller flap. The donor sites were primarily closed in all cases. One patient had delayed wound healing, and the secondary wound healed using conservative dressing changes. The other 6 flaps had no complications. The average follow-up time was 5.3 months (range, 1–9 months). Muscle weakness and compromised ambulation in the affected lower extremities were not observed in any of the patients. Furthermore, all 7 patients had no tumor recurrence, prosthesis exposure, and infection events in the sacrococcygeal region.

Conclusions
The chimeric perforator propeller flap may be an option for reconstructing complex soft tissue defects in the sacrococcygeal region.
Severe Upper Lid Fornix Prolapse After a Ptosis Repair in Floppy Eyelid Syndrome
Authors: Radulovich Nicholas P. , Michels Kevin S. 
Published: October 2023

AbstractPatients with profound floppy eyelid syndrome (FES) may experience challenges achieving eyelid and tarsal stability in the setting of severe ptosis. A 43-year-old woman with sleep apnea presented to clinic with difficulties driving because of droopy eyelids. She also experienced chronic tearing, crusting, and discharge of the eyes. She was diagnosed with severe FES and significant ptosis. She underwent a wedge excision of the upper lid in the medial and lateral aspect of the upper lid. This was followed by a ptosis repair that resulted in complete upper lid fornix obliteration causing the conjunctiva to obstruct the patient's pupils. The patient's symptoms ultimately improved after a definitive fornix reconstruction. Her visual field symptoms were improved with 1-year follow-up. To our knowledge, this is the first report in the literature of a prolapsed fornix resulting in vision obstruction after floppy eyelid repair via a wedge excision followed by a ptosis repair via an external levator advancement. Given these unusual findings for the patient's age, further investigations into treatment management may be necessary to mitigate eyelid reconstruction complications in younger patients with FES.
Technical and Clinical Differences Between Transgender and Cisgender Females Undergoing Breast Augmentation
Authors: Torres Perez-Iglesias Carolina A. , Heyman Annie , Koh Daniel J. , Medina Nilton , Roh Daniel S. , Slama Jaromir 
Published: October 2023

Background
Gender-affirming surgery is a quickly expanding field. However, it is facing a shortage of specialized surgeons for a population exceeding 1.4 million individuals. Many studies comparing outcomes between cisgender and transgender patients fail to describe the technical differences of the operation. Breast augmentation in the transgender female patient involves important anatomical, technical, and clinical features that differ from the cisgender female. In this study, we aimed to describe and compare these characteristics between these 2 groups to better inform the new generation of gender-affirming surgeons.

Methods
A retrospective cohort study of patients who underwent primary breast augmentation between 2009 and 2019 at a specialized tertiary center for transgender care was performed. Mastopexy, secondary augmentation, and reconstructive procedures were excluded. Demographic, operative, and clinical data were collected from medical records. All patients had a minimum of 1 year of follow-up after the initial surgery. Bivariate analysis was performed.

Results
A total of 250 cisgender females and 153 transgender females were included. The transgender group showed higher rates of smoking (P < 0.0001), immunosuppression (P < 0.0001), obesity (P < 0.0001), mental health disorders (P < 0.0001), and hypertension (P = 0.002). Median base width (P < 0.0001), sternal notch to nipple distance (P < 0.0001), and implant size (500 mL [interquartile range, 425–600 mL] vs 350 mL [interquartile range, 325–385 mL]; P < 0.0001) were larger in transgender patients. Transgender patients also demonstrated a stronger correlation between implant size and body surface area (r = 0.71, P < 0.0001). Readmission, reoperation, and complication rates were similar between the groups; however, transgender females had a higher incidence of surgical site infections (3.9% vs 0.4%, P < 0.013). Capsular contracture was the most common complication and indication for reoperation in both groups.

Conclusions
There are important anatomical, clinical, and technical differences between reconstructive gender-affirming breast augmentation in transgender female patients and cosmetic breast augmentation in the cisgender female. The gender-affirming surgeon must know these differences to provide the best quality of care and help patients achieve better congruence between their gender identity and body image.
Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of complex traits in pig
Authors: Xu Zhiting , Lin Qing , Cai Xiaodian , Zhong Zhanming , Li Bingjie , Teng Jinyan , Zeng Haonan , Gao Yahui , Cai Zexi , Wang Xiaoqing , Shi Liangyu , Wang Xue , Wang Yi , Zhang Zipeng , Lin Yu , Liu Shuli , Yin Hongwei , Bai Zhonghao , Wei Chen , Zhou Jun , Zhang Wenjing , Zhang Xiaoke , Shi Shaolei , Wu Jun , Diao Shuqi , Liu Yuqiang , Pan Xiangchun , Feng Xueyan , Liu Ruiqi , Su Zhanqin , Chang Chengjie , Zhu Qianghui , Wu Yuwei ,   The PigGTEx Consortium, Zhou Zhongyin , Bai Lijing , Li Kui , Wang Qishan , Pan Yuchun , Xu Zhong , Peng Xianwen , Mei Shuqi , Mo Delin , Liu Xiaohong , Zhang Hao , Yuan Xiaolong , Liu Yang , Liu George E. , Su Guosheng , Sahana Goutam , Lund Mogens Sandø , Ma Li , Xiang Ruidong , Shen Xia , Li Pinghua , Huang Ruihuang , Ballester Maria , Crespo-Piazuelo Daniel , Amills Marcel , Clop Alex , Karlskov-Mortensen Peter , Fredholm Merete , Tang Guoqing , Li Mingzhou , Li Xuewei , Ding Xiangdong , Li Jiaqi , Chen Yaosheng , Zhang Qin , Zhao Yunxiang , Zhao Fuping , Fang Lingzhao , Zhang Zhe 
Published: October 2023

AbstractUnderstanding the molecular and cellular mechanisms that underlie complex traits in pigs is crucial for enhancing their genetic improvement program and unleashing their substantial potentials in human biomedicine research. Here, we conducted a meta-GWAS analysis for 232 complex traits with 28.3 million imputed whole-genome sequence variants in 70,328 individuals from 14 pig breeds. We identified a total of 6,878 genomic regions associated with 139 complex traits. By integrating with the Pig Genotype-Tissue Expression (PigGTEx) resource, we systemically explored the biological context and regulatory circuits through which these trait-associated variants act and finally prioritized 16,664 variant-gene-tissue-trait circuits. For instance, rs344053754 regulates the expression ofUGT2B31in the liver by affecting the activity of regulatory elements and ultimately influences litter weight at weaning. Furthermore, we investigated the conservation of genetic and regulatory mechanisms underlying 136 human traits and 232 pig traits. Overall, our multi-breed meta-GWAS in pigs provides invaluable resources and novel insights for understanding the regulatory and evolutionary mechanisms of complex traits in both pigs and humans.
Double-strand break repair-associated intragenic deletions and tandem duplications suggest the architecture of the repair replication fork
Authors: Dalin Simona , Webster Sophie , Sugawara Neal , Zhang Shu , Wu Qiuqin , Cui Tracy , Liang Victoria , Beroukhim Rameen , Haber James E. 
Published: October 2023

AbstractDouble-strand break (DSB) repair is associated with a 1000-fold increase in mutations compared to normal replication of the same sequences. In budding yeast, repair of an HO endonuclease-induced DSB at theMATα locus can be repaired by using a homologous, heterochromaticHMR::Kl-URA3donor harboring a transcriptionally silencedURA3gene, resulting in aMAT::URA3(Ura+) repair product whereURA3is expressed. Repair-associatedura3-mutations can be selected by resistance to 5-fluoroorotic acid (FOA). Using this system, we find that a major class of mutations are -1 deletions, almost always in homonucleotide runs, but there are few +1 insertions. In contrast, +1 and -1 insertions in homonucleotide runs are nearly equal among spontaneous mutations. Approximately 10% of repair-associated mutations are interchromosomal template switches (ICTS), even though theK. lactis URA3sequence embedded inHMRis only 72% identical withS. cerevisiae ura3-52sequences on a different chromosome. ICTS events begin and end in regions of short microhomology, averaging 7 bp. Long microhomologies are favored, but some ICTS junctions are as short as 2 bp. Both repair-associated intragenic deletions (IDs) and tandem duplications (TDs) are recovered, with junctions sharing short stretches of, on average, 6 bp of microhomology. Intragenic deletions are more than 5 times more frequent than TDs. IDs have a mean length of 60 bp, but, surprisingly there are almost no deletions shorter than 25 bp. In contrast, TDs average only 12 bp. The usage of microhomologies among intragenic deletions is not strongly influenced by the degree of adjacent homeology. Together, these data provide a picture of the structure of the repair replication fork. We suggest that IDs and TDs occur within the migrating D-loop in which DNA polymerase δ copies the template, where the 3’ end of a partly copied new DNA strand can dissociate and anneal with a single-stranded region of microhomology that lies either in front or behind the 3’ end, within the open structure of a migrating D-loop. Our data suggest that ∼100 bp ahead of the polymerase is “open,” but that part of the repair replication apparatus remains bound in the 25 bp ahead of the newly copied DNA, preventing annealing. In contrast, the template region behind the polymerase appears to be rapidly reannealed, limiting template switching to a very short region.
CUDASW++4.0: Ultra-fast GPU-based Smith-Waterman Protein Sequence Database Search
Authors: Schmidt Bertil , Kallenborn Felix , Chacon Alejandro , Hundt Christian 
Published: October 2023

AbstractBackgroundThe maximal sensitivity for local pairwise alignment makes the Smith-Waterman algorithm a popular choice for protein sequence database search. However, its quadratic time complexity makes it compute-intensive. Unfortunately, current state-of-the-art software tools are not able to leverage the massively parallel processing capabilities of modern GPUs with close-to-peak performance. This motivates the need for more efficient implementations.ResultsCUDASW++4.0 is a fast software tool for scanning protein sequence databases with the Smith-Waterman algorithm on CUDA-enabled GPUs. Our approach achieves high efficiency for dynamic programming-based alignment computation by minimizing memory accesses and instructions. We provide both efficient matrix tiling, and sequence database partitioning schemes, and exploit next generation floating point arithmetic and novel DPX instructions. This leads to close-to-peak performance on modern GPU generations (Ampere, Ada, Hopper) with throughput rates of up to 1.94 TCUPS, 5.01 TCUPS, 5.71 TCUPS on an A100, L40S, and H100, respectively. Evaluation on the Swiss-Prot, UniRef50, and TrEMBL databases shows that CUDASW++4.0 gains over an order-of-magnitude performance improvements over previous GPU-based approaches (CUDASW++3.0, ADEPT). In addition, our algorithm demonstrates significant speedups over top-performing CPU-based tools (BLASTP, SWIPE, SWIMM2.0), can exploit multi-GPU nodes with linear scaling, and features an impressive energy efficiency of up to 15.7 GCUPS/Watt.ConclusionCUDASW++4.0 changes the standing of GPUs in protein sequence database search with Smith-Waterman alignment by providing close-to-peak performance on modern GPUs. It is freely available athttps://github.com/asbschmidt/CUDASW4.
Enhancing Disease Risk Gene Discovery by Integrating Transcription Factor-Linked Trans-located Variants into Transcriptome-Wide Association Analyses
Authors: He Jingni , Perera Deshan , Wen Wanqing , Ping Jie , Li Qing , Lyu Linshuoshuo , Chen Zhishan , Shu Xiang , Long Jirong , Cai Qiuyin , Shu Xiao-Ou , Zheng Wei , Long Quan , Guo Xingyi 
Published: October 2023

AbstractTranscriptome-wide association studies (TWAS) have been successful in identifying disease susceptibility genes by integrating cis-variants predicted gene expression with genome-wide association studies (GWAS) data. However, trans-located variants for predicting gene expression remain largely unexplored. Here, we introduce transTF-TWAS, which incorporates transcription factor (TF)-linked trans-located variants to enhance model building. Using data from the Genotype-Tissue Expression project, we predict gene expression and alternative splicing and applied these models to large GWAS datasets for breast, prostate, and lung cancers. We demonstrate that transTF-TWAS outperforms other existing TWAS approaches in both constructing gene prediction models and identifying disease-associated genes, as evidenced by simulations and real data analysis. Our transTF-TWAS approach significantly contributes to the discovery of disease risk genes. Findings from this study have shed new light on several genetically driven key regulators and their associated regulatory networks underlying disease susceptibility.