bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of carbon substrate competition among heterotrophic microorganisms
Authors: McNichol Samuel M , Sanchez-Quete Fernando , Loeb Stephanie K , Teske Andreas P , Shah Walter Sunita R , Mahmoudi Nagissa 
Published: January 2024

Abstract
Growing evidence suggests that interactions among heterotrophic microorganisms influence the efficiency and rate of organic matter turnover. These interactions are dynamic and shaped by the composition and availability of resources in their surrounding environment. Heterotrophic microorganisms inhabiting marine environments often encounter fluctuations in the quality and quantity of carbon inputs, ranging from simple sugars to large, complex compounds. Here, we experimentally tested how the chemical complexity of carbon substrates affects competition and growth dynamics between two heterotrophic marine isolates. We tracked cell density using species-specific polymerase chain reaction (PCR) assays and measured rates of microbial CO2 production along with associated isotopic signatures (13C and 14C) to quantify the impact of these interactions on organic matter remineralization. The observed cell densities revealed substrate-driven interactions: one species exhibited a competitive advantage and quickly outgrew the other when incubated with a labile compound whereas both species seemed to coexist harmoniously in the presence of more complex organic matter. Rates of CO2 respiration revealed that coincubation of these isolates enhanced organic matter turnover, sometimes by nearly 2-fold, compared to their incubation as mono-cultures. Isotopic signatures of respired CO2 indicated that coincubation resulted in a greater remineralization of macromolecular organic matter. These results demonstrate that simple substrates promote competition whereas high substrate complexity reduces competitiveness and promotes the partitioning of degradative activities into distinct niches, facilitating coordinated utilization of the carbon pool. Taken together, this study yields new insight into how the quality of organic matter plays a pivotal role in determining microbial interactions within marine environments.
Are associations between physical activity and bone mineral density in adults sex- and age-dependent? An analysis of the UK Biobank study
Authors: Montgomery Gallin , Yusuf Mohamed , Cooper Rachel , Ireland Alex 
Published: January 2024

Abstract
Although physical activity (PA) is recognized as a key bone mass determinant across life, athlete studies suggest that it may be less effective in women and older individuals. This has not been explored within the general population. We aimed to address this knowledge gap using data from the UK Biobank Study, a large population-based study of middle-aged and older adults. Free-living PA data collected at 100 Hz for 7 d using wrist-worn accelerometers were classified as sedentary behavior (0–29 milligravities [mg]), light (30–124 mg), or moderate-to-vigorous PA (125 + mg). LS and FN-BMD were assessed using DXA. The associations between PA and BMD were assessed using linear regression models, with formal assessments of sex and age interactions undertaken and adjustments made for accelerometer wear time, height, body mass index, education, ethnicity, disability, and (in women only) menopausal status. In total, 15 133 UK Biobank participants (52% women) had complete PA, bone, and covariate data. In this sample, greater overall and moderate-to-vigorous PA was associated with higher LS BMD. In women, these associations were typically weaker in older individuals, for example, regression coefficients in women aged 70 yr or older were ~50% lower than at 45–54 yr (age-by-PA interactions P &lt; .01 in all models). Similar associations were observed in basic but not full models for FN BMD. Greater sedentary time was associated with lower LS BMD in men only, and greater light PA and sedentary time were associated with higher and lower FN BMD, respectively, in both sexes. These results suggest that associations between PA and bone health at clinically-relevant sites are weaker in older than younger women. That positive associations are evident between overall and moderate-vigorous PA and FN BMD even in women ≥70 yr suggests that PA for bone health should still be promoted in older women.
Computational investigation of thermal process in radiated nanofluid modulation influenced by nanoparticles (Al2O3) and molecular (H2O) diameters
Authors: Bani-Fwaz Mutasem Z ,   Adnan , Mahmood Zafar , Bilal Muhammad , EI-Zahhar Adel A , Khan Ilyas , Niazai Shafiullah 
Published: January 2024

Abstract
The study of variety of Newtonian nanofluids subject to various physical model parameters gained much interest of engineers and scientists. Owing to their coolant and absorption characteristics, these are broadly found in chemical engineering, biomedical engineering (expansion and contraction of veins and arteries), detection of cancer cells through magnetic nanoparticles, microchips, and particularly in petroleum industry. This study focuses on investigation of nanofluid heat transfer applications inside a channel formed by expanding/contracting walls. A new heat transport model is introduced by adding the effects of nanoparticles and molecular diameters, thermal radiations, and walls permeability. Then, numerical code for the model is developed and executed to analyze the dynamics of the model from physical aspects. For expanding (${\alpha }_1 = 1.0,2.0,3.0,4.0$) and contracting (${\alpha }_1 = - 1.0, - 2.0, - 3.0, - 4.0$) walls, the velocity is examined maximum in the channel center. However, the fluid movement in the working domain is in reverse proportion for ${Re} = 1.0,3.0,5.0,7.0$. Further, high absorbent walls (${A}_1 = 0.1,0.3,0.5,0.7$) controlled the motion for both ${\alpha }_1 &gt; 0$ and ${\alpha }_1 &lt; 0$, respectively. The addition of thermal radiation number ${Rd} = 0.1,0.3,0.5,0.7$ played the role of catalytic parameter which imperatively increased the fluid temperature. Further, contracting walls and temperature ratio number ${\theta }_r = 0.1,0.3,0.5,0.7$ reduced the temperature and this decrease is rapid in conventional fluid.
Effects of mosquito age and batch size on knockdown and mortality of laboratory-reared Anopheles dirus, Anopheles minimus, and wild-caught Anopheles harrisoni (Diptera: Culicidae) exposed to transfluthrin using WHO tube and CDC bottle bioassays
Authors: Saeung Manop , Ngoen-Klan Ratchadawan , Yan Chanly , Kerdsawang Jutamas , Nararak Jirod , Manguin Sylvie , Hii Jeffrey , Chareonviriyaphap Theeraphap 
Published: January 2024

Abstract
WHO tube and CDC bottle bioassays are currently available for insecticide resistance monitoring and malaria transmission research. Multiple parameters including mosquito density, age, and nutritional status may affect the readout in these bioassays’ tests. This study aims to assess the effects of experimental factors on knockdown and mortality measurements in dominant malaria vectors in Thailand following exposure to sublethal and lethal doses of transfluthrin. The effects of (i) 3 different mosquito batch sizes (5, 10, and 20 individuals) and (ii) 2 age groups (3–5 and 20–23 days old) on outcomes measured using the WHO tube (14.7 µg/cm2) and CDC bottle bioassay discriminating concentration (0.006 µg/cm2) against 2 laboratory strains: Anopheles dirus Peyton & Harrison and Anopheles minimus Theobald (species A) and wild-caught Anopheles harrisoni Harbach & Manguin (species C). Our results showed higher knockdown at 1-h exposure using WHO tube and CDC bottle bioassays containing 20 individuals compared to batches containing 10 and 5 individuals. Older mosquitoes showed greater susceptibility than younger test population, especially for An. mininus. Our study supports WHO recommendations for using 3- to 5-day-old mosquitoes. It also validates Praulin et al. (2022) proposal to divide the cohort into smaller batches with more test replicates when it is not practicable to test 25 mosquitoes per replicate.
Robot-assisted radical prostatectomy in a patient with prostate cancer complicated by benign prostate hypertrophy with middle lobe hypertrophy
Authors: Kawamura Yoshiaki , Uchida Takato , Umemoto Tatsuya , Nakajima Nobuyuki , Nitta Masahiro , Hasegawa Masanori , Shoji Sunao , Miyajima Akira 
Published: January 2024

Abstract
Robot-assisted radical prostatectomy (RARP) is difficult in patients with benign prostatic hyperplasia (BPH), a condition causing frequent urination, because of the large prostate volume and particularly true when BPH is accompanied by an enlarged middle lobe. To overcome this difficulty, some surgeons elevate the middle lobe with a third arm or tow the urethral catheter to the edge to identify the resection line. Herein, we describe a method for lifting a prostate with an enlarged middle lobe, which was successfully applied in a patient with prostate cancer and BPH. This technique can help identify the resection line between the bladder and prostate, reducing surgical difficulty and the number of unnecessary sutures.
Generalization Across Experimental Parameters in Neural Network Analysis of High-Resolution Transmission Electron Microscopy Datasets
Authors: Sytwu Katherine , Rangel DaCosta Luis , Scott Mary C 
Published: January 2024

Abstract
Neural networks are promising tools for high-throughput and accurate transmission electron microscopy (TEM) analysis of nanomaterials, but are known to generalize poorly on data that is “out-of-distribution” from their training data. Given the limited set of image features typically seen in high-resolution TEM imaging, it is unclear which images are considered out-of-distribution from others. Here, we investigate how the choice of metadata features in the training dataset influences neural network performance, focusing on the example task of nanoparticle segmentation. We train and validate neural networks across curated, experimentally collected high-resolution TEM image datasets of nanoparticles under various imaging and material parameters, including magnification, dosage, nanoparticle diameter, and nanoparticle material. Overall, we find that our neural networks are not robust across microscope parameters, but do generalize across certain sample parameters. Additionally, data preprocessing can have unintended consequences on neural network generalization. Our results highlight the need to understand how dataset features affect deployment of data-driven algorithms.
Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening
Authors: Gezelius Henrik , Enblad Anna Pia , Lundmark Anders , Åberg Martin , Blom Kristin , Rudfeldt Jakob , Raine Amanda , Harila Arja , Rendo Verónica , Heinäniemi Merja , Andersson Claes , Nordlund Jessica 
Published: January 2024

Abstract
Functional precision medicine (FPM) aims to optimize patient-specific drug selection based on the unique characteristics of their cancer cells. Recent advancements in high throughput ex vivo drug profiling have accelerated interest in FPM. Here, we present a proof-of-concept study for an integrated experimental system that incorporates ex vivo treatment response with a single-cell gene expression output enabling barcoding of several drug conditions in one single-cell sequencing experiment. We demonstrate this through a proof-of-concept investigation focusing on the glucocorticoid-resistant acute lymphoblastic leukemia (ALL) E/R+ Reh cell line. Three different single-cell transcriptome sequencing (scRNA-seq) approaches were evaluated, each exhibiting high cell recovery and accurate tagging of distinct drug conditions. Notably, our comprehensive analysis revealed variations in library complexity, sensitivity (gene detection), and differential gene expression detection across the methods. Despite these differences, we identified a substantial transcriptional response to fludarabine, a highly relevant drug for treating high-risk ALL, which was consistently recapitulated by all three methods. These findings highlight the potential of our integrated approach for studying drug responses at the single-cell level and emphasize the importance of method selection in scRNA-seq studies. Finally, our data encompassing 27 327 cells are freely available to extend to future scRNA-seq methodological comparisons.
scBiG for representation learning of single-cell gene expression data based on bipartite graph embedding
Authors: Li Ting , Qian Kun , Wang Xiang , Li Wei Vivian , Li Hongwei 
Published: January 2024

Abstract
Analyzing single-cell RNA sequencing (scRNA-seq) data remains a challenge due to its high dimensionality, sparsity and technical noise. Recognizing the benefits of dimensionality reduction in simplifying complexity and enhancing the signal-to-noise ratio, we introduce scBiG, a novel graph node embedding method designed for representation learning in scRNA-seq data. scBiG establishes a bipartite graph connecting cells and expressed genes, and then constructs a multilayer graph convolutional network to learn cell and gene embeddings. Through a series of extensive experiments, we demonstrate that scBiG surpasses commonly used dimensionality reduction techniques in various analytical tasks. Downstream tasks encompass unsupervised cell clustering, cell trajectory inference, gene expression reconstruction and gene co-expression analysis. Additionally, scBiG exhibits notable computational efficiency and scalability. In summary, scBiG offers a useful graph neural network framework for representation learning in scRNA-seq data, empowering a diverse array of downstream analyses.
Early vs delayed insertion of penile prosthesis in patients with refractory priapism: a systematic review and meta-analysis
Authors: Elmarasi Mohamed , Alsaeedi Ahmad , Elmakaty Ibrahim , Elsayed Basel , Khalil Ibrahim A , Aldeeb Maya , Khalafalla Kareim , Al Kubaisi Khalid , Arafa Mohamed , Majzoub Ahmed 
Published: January 2024

Abstract

Introduction
Refractory priapism, characterized by persistent and prolonged painful erections despite initial treatment maneuvers, can significantly impair erectile function secondary to ischemia-induced corporal tissue fibrosis. These patients will likely require subsequent penile prosthesis (PP) surgery to regain sexual activity, yet consensus regarding the optimal timing of implantation remains lacking.

Objectives
To evaluate and compare the clinical outcomes associated with early vs delayed PP implantation in individuals with priapism-induced erectile dysfunction (ED).

Methods
We included studies that focused on refractory priapism leading to ED and its management with PP implantation. We assessed cohort study bias with a risk-of-bias tool and case series bias with the modified Newcastle-Ottawa Scale. Pooled odds ratios (ORs) were calculated by a fixed-effect model.

Results
We included 9 studies, comprising 4 cohort studies and 5 case series, involving a total of 278 patients. Total complications were higher in the delayed group (OR, 4.16; 95% CI, 2.77-6.26). Fibrosis was significantly more pronounced in the delayed group (OR, 118.18; 95% CI, 20.06-696.32). The odds of erosion, infections, and penile injury did not show statistically significant differences between the groups (OR, 2.52 [95% CI, 0.67-9.49], 0.89 [0.38-2.10], 1.83 [0.79-4.26], respectively). Patients’ satisfaction resulted in a pooled OR of 0.15 (95% CI, 0.04-0.49) in favor of the early PP insertion group.

Conclusion
The results from this study favor an early approach to ED (within 30 days) following ischemic priapism. However, it is important to consider patients’ preferences, values, and psychological factors to make an informed decision.
Degenerative Cervical Myelopathy
Authors: Gallagher Daniel O. , Taghlabi Khaled M. , Bondar Kevin , Saifi Comron 
Published: January 2024

Study Design:
Narrative review.

Objective:
To provide an overview of the evaluation and diagnosis of degenerative cervical myelopathy (DCM).

Summary of Background Data:
DCM describes several etiologies of degenerative, nontraumatic spinal cord impairment. Early diagnosis and intervention can decrease neurological decline.

Methods:
An extensive literature review was conducted.

Results:
The incidence and prevalence of DCM are increasing worldwide. Asymptomatic spinal cord compression can progress to cervical myelopathy. Static and dynamic factors contribute to spinal cord compression. Patients frequently present with decreased manual dexterity, gait instability, and neck pain. On physical exam, patients frequently present with upper motor neuron signs, a Lhermitte sign, a failed Romberg test, global proprioceptive dysfunction, and decreased pain sensation. Anatomic variation may complicate physical exam interpretation. The modified Japanese Orthopaedic Association Scale and Nurick Classification, based on functional impairment, provide diagnostic utility. Magnetic Resonance Imaging imaging is useful in narrowing the differential diagnosis, evaluating the severity of neurological impairment, and predicting disease progression.

Conclusions:
Understanding the pathophysiology of DCM and the diagnostic utility of the signs and symptoms of DCM is critical. The decision for anterior cervical discectomy and fusion (ACDF), laminoplasty, or combined ACDF and posterior cervical fusion is individualized for each patient.
The Benefits of Using Platelet-rich Plasma with Dermal Substitutes for Extremity Posttraumatic Skin Defects: A Short-term Outcome
Authors: Darwish Yasmine G. , Gharbia Mohamed , Sobhi Ahmed M. , Aborady Ahmed F. 
Published: January 2024

Background:
Skin injuries are very common. Skin grafting is an ongoing wound management procedure. The artificial dermis, PELNAC, has been considered in the treatment of several acute and chronic skin injuries. Platelet-rich plasma (PRP) is blood plasma with a platelet count higher than the baseline. It is presumed to act in a synergetic pattern to promote the healing of wounds. This study was conducted to assess the potential benefit of adding PRP to PELNAC as adjuvant therapy in treating posttraumatic skin.

Methods:
In this study, adult patients who were admitted to the hospital with extremity traumatic skin and soft tissue defects with exposed bare bone, exposed tendons, or exposed cartilage in the period between October 2019 and March 2021 were allocated to either being managed with dermal substitute (PELNAC) together with PRP (group I) or PELNAC alone (group II).

Results:
Patients in group I showed a higher mean graft take rate and a lower mean time for neovascularization of the acellular dermal matrix, with a statistically highly significant difference. The Vancouver Scar Scale values showed no significant difference in either group. The PRP-treated group showed statistically significant shorter hospital stays.

Conclusions:
The addition of PRP to the treatment protocol showed better outcomes in terms of graft take rate, time for neovascularization of acellular dermal matrix, and length of hospital stay, with no side effects. The present study findings emphasize the promising outcome of PRP in addition to the standard treatment of complex wounds to achieve rapid and safe healing.
Nontyphoidal Salmonella Outbreaks Associated With Chocolate Consumption: A Systematic Review
Authors: Patà Zacharie , Faré Pietro B. , Lava Sebastiano A. G. , Milani Gregorio P. , Bianchetti Mario G. , Janett Simone , Hunjan Isabella , Kottanattu Lisa 
Published: January 2024

Background:
A large, cross-border outbreak of nontyphoidal salmonellosis connected to chocolate product consumption was recently reported. This occurrence motivated us to conduct a comprehensive review of existing literature concerning outbreaks of nontyphoidal salmonellosis associated with chocolate consumption.

Methods:
We performed a systematic review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines (PROSPERO CRD42022369023) in 3 databases: U.S. National Library of Medicine, Web of Science and Excerpta Medica. Google Scholar and the bibliography of each identified report were also screened. Eligible were articles published after 1970, describing outbreaks of more than 10 patients with a nontyphoidal salmonellosis associated with chocolate consumption.

Results:
Twenty-three articles were included, which described 12 outbreaks involving a total of 3266 patients. All outbreaks occurred in high-income countries: 1 was limited to 1 city, 6 involved 1 country and the remaining 5 involved 2 or more countries. Six outbreaks peaked in winter, 3 in autumn, 2 in spring and 1 in summer. Children were mainly affected. No predominant serotype was identified.

Conclusions:
Our data documents that chocolate is an optimal medium for the transmission of nontyphoidal salmonellosis. A connected worldwide reporting system including high-income, middle-income and low-income countries is crucial to detect infectious diseases outbreaks in an early phase and avoid their spread.
Impact of preoperative infection on the outcomes of liver transplant recipients: a national propensity score-matched retrospective cohort study in China
Authors: Xiang Ze , Song Yisu , Liu Jianrong , Xu Chenhao , Zhou Zhisheng , Li Jiarui , Su Renyi , Shu Wenzhi , Lu Zhengyang , Wei Xuyong , Yang Jiayin , Yang Yang , Zheng Shusen , Xu Xiao 
Published: January 2024

Background:
Impact of preoperative infection on liver transplantation (LT) needs further investigation.

Materials and methods:
From 1 January 2015 to 31 December 2022, 24 122 eligible patients receiving LT were enrolled from the China Liver Transplant Registry database. The outcomes of LT were compared after using the propensity score-matched analysis.

Results:
Compared to the noninfection group, patients in the infection group were more likely to have postoperative effusion, infection, abdominal bleeding, and biliary complications (all P<0.01), and they had shorter 30-day, 90-day survival, and overall survival (all P<0.01). Cox proportional hazards regression analysis revealed that MELD score and cold ischemia time were risk factors for the overall survival in the infection group (both P<0.05). Besides, compared to the nonpulmonary group, patients in the pulmonary group were more likely to have postoperative effusion and infection (both P<0.0001), and less likely to have postoperative abscess and early allograft dysfunction (both P<0.05). Patients in the nonabdominal group also had a higher proportion of postoperative infection than those in the abdominal group (P<0.05). Furthermore, compared to the number=1 group, patients in the number ≥2 group were more prone to postoperative effusion and infection (both P<0.01), and they also had shorter 30-day and 90-day survival (both P<0.05).

Conclusion:
Preoperative infection can result in a higher incidence of early postoperative complications and shorter survival in liver transplant recipients. The types and number of infection sites will also influence the prognosis of liver transplant recipients.
Surgical Treatment of Malignant Peripheral Nerve Sheath Tumor of the Scalp With Intracranial and Extracranial Extension
Authors: Cheng Ting-An , Shieh Shyh-Jou 
Published: January 2024

Abstract
Malignant peripheral nerve sheath tumors of the scalp are rare neoplasms of the peripheral nervous system. Here, we describe an unusual malignant peripheral nerve sheath tumor of the scalp in an 84-year-old Asian man. The tumor was associated with bony destruction, intracranial, and extracranial extension. Trans-arterial embolization was done twice preoperatively. En block excision was performed and the dura and soft tissue defect were reconstructed by anterolateral thigh free fasciocutaneous flap. There is no recurrence and the wound healed well during follow-up.