bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assembly processes and functional diversity of marine protists and their rare biosphere
Authors: Ramond Pierre , Siano Raffaele , Sourisseau Marc , Logares Ramiro 
Published: July 2023

Abstract
Background
The mechanisms shaping the rare microbial biosphere and its role in ecosystems remain unclear. We developed an approach to study ecological patterns in the rare biosphere and use it on a vast collection of marine microbiomes, sampled in coastal ecosystems at a regional scale. We study the assembly processes, and the ecological strategies constituting the rare protistan biosphere. Using the phylogeny and morpho-trophic traits of these protists, we also explore their functional potential.

Results
Taxonomic community composition remained stable along rank abundance curves. Conditionally rare taxa, driven by selection processes, and transiently rare taxa, with stochastic distributions, were evidenced along the rank abundance curves of all size-fractions. Specific taxa within the divisions Sagenista, Picozoa, Telonemia, and Choanoflagellida were rare across time and space. The distribution of traits along rank abundance curves outlined a high functional redundancy between rare and abundant protists. Nevertheless, trophic traits illustrated an interplay between the trophic groups of different size-fractions.

Conclusions
Our results suggest that rare and abundant protists are evolutionary closely related, most notably due to the high microdiversity found in the rare biosphere. We evidenced a succession of assembly processes and strategies of rarity along rank abundance curves that we hypothesize to be common to most microbiomes at the regional scale. Despite high functional redundancy in the rare protistan biosphere, permanently rare protists were evidenced, and they could play critical functions as bacterivores and decomposers from within the rare biosphere. Finally, changes in the composition of the rare protistan biosphere could be influenced by the trophic regime of aquatic ecosystems. Our work contributes to understanding the role of rare protists in microbiomes.
Emerging nano-scale delivery systems for the treatment of osteoporosis
Authors: Dayanandan Anoop Puthiyoth , Cho Woong Jin , Kang Hyemin , Bello Alvin Bacero , Kim Byoung Ju , Arai Yoshie , Lee Soo-Hong 
Published: July 2023

Abstract
Osteoporosis is a pathological condition characterized by an accelerated bone resorption rate, resulting in decreased bone density and increased susceptibility to fractures, particularly among the elderly population. While conventional treatments for osteoporosis have shown efficacy, they are associated with certain limitations, including limited drug bioavailability, non-specific administration, and the occurrence of adverse effects. In recent years, nanoparticle-based drug delivery systems have emerged as a promising approach for managing osteoporosis. Nanoparticles possess unique physicochemical properties, such as a small size, large surface area-to-volume ratio, and tunable surface characteristics, which enable them to overcome the limitations of conventional therapies. These nanoparticles offer several advantages, including enhanced drug stability, controlled release kinetics, targeted bone tissue delivery, and improved drug bioavailability. This comprehensive review aims to provide insights into the recent advancements in nanoparticle-based therapy for osteoporosis. It elucidates the various types of nanoparticles employed in this context, including silica, polymeric, solid lipid, and metallic nanoparticles, along with their specific processing techniques and inherent properties that render them suitable as potential drug carriers for osteoporosis treatment. Furthermore, this review discusses the challenges and future suggestions associated with the development and translation of nanoparticle drug delivery systems for clinical use. These challenges encompass issues such as scalability, safety assessment, and regulatory considerations. However, despite these challenges, the utilization of nanoparticle-based drug delivery systems holds immense promise in revolutionizing the field of osteoporosis management by enabling more effective and targeted therapies, ultimately leading to improved patient outcomes.
Design, printing optimization, and material testing of a 3D-printed nasal osteotomy task trainer
Authors: Schlegel Lauren , Malani Eric , Belko Sara , Kumar Ayan , Barbarite Eric , Krein Howard , Heffelfinger Ryan , Hutchinson Morgan , Pugliese Robert 
Published: July 2023

Abstract
Background
For difficult or rare procedures, simulation offers an opportunity to provide education and training. In developing an adequate model to utilize in simulation, 3D printing has emerged as a useful technology to provide detailed, accessible, and high-fidelity models. Nasal osteotomy is an essential step in many rhinoplasty surgeries, yet it can be challenging to perform and difficult to receive adequate exposure to this nuanced portion of the procedure. As it currently stands, there are limited opportunities to practice nasal osteotomy due to the reliance on cadaveric bones, which are expensive, difficult to obtain, and require appropriate facilities and personnel. While previous designs have been developed, these models leave room for improvement in printing efficiency, cost, and material performance. This manuscript aims to describe the methodology for the design of an updated nasal osteotomy training model derived from anatomic data and optimized for printability, usability, and fidelity. Additionally, an analysis of multiple commercially available 3D printing materials and technologies was conducted to determine which offered superior equivalency to bone.

Methods
This model was updated from a first-generation model previously described to include a more usable base and form, reduce irrelevant structures, and optimize geometry for 3D printing, while maintaining the nasal bones with added stabilizers essential for function and fidelity. For the material comparison, this updated model was printed in five materials: Ultimaker Polylactic Acid, 3D Printlife ALGA, 3DXTECH SimuBone, FibreTuff, and FormLabs Durable V2. Facial plastic surgeons tested the models in a blinded, randomized fashion and completed surveys assessing tactile feedback, audio feedback, material limitation, and overall value.

Results
A model optimizing printability while maintaining quality in the area of interest was developed. In the material comparison, SimuBone emerged as the top choice amongst the evaluating physicians in an experience-based subjective comparison to human bone during a simulated osteotomy procedure using the updated model.

Conclusion
The updated midface model that was user-centered, low-cost, and printable was designed. In material testing, Simubone was rated above other materials to have a more realistic feel.
Feasibility of manufacture of chimeric antigen receptor-regulatory T cells from patients with end-stage renal disease
Authors: Bastian Hervé , Lounnas-Mourey Nadia , Heimendinger Pierre , Hsu Benjamin L. , Schreeb Katharina H. , Chapman Claire , Culme-Seymour Emily , Atkinson Gillian F. , Cantarovich Diego 
Published: July 2023

Abstract
Background
Gene-modified cell therapy with regulatory T cells (Tregs) is a promising approach to prevent graft rejection and induce immunological tolerance in organ transplantation. We are developing a cell therapy comprising autologous naïve Tregs that are isolated from leukapheresate, transduced with lentiviral vector encoding a chimeric antigen receptor (CAR) recognising human leukocyte antigen class I molecule A*02 (HLA-A*02), and expanded ex vivo before cryopreservation as resultant drug product (TX200-TR101). In an ongoing first-in-human study (NCT04817774), kidney transplant recipients will receive a single infusion of TX200-TR101 2–3 months after transplantation. The phase 0 study described here evaluated the feasibility of manufacture of TX200-TR101 for the target population, i.e., end-stage renal disease (ESRD) necessitating kidney transplantation. Participants in this study did not receive an infusion of drug product.

Methods
Four patients with ESRD and HLA-A*02 negative typing underwent leukapheresis to collect starting material for manufacture of TX200-TR101. Manufacturing success criteria were predefined as a batch of CAR-Tregs with cell quantity in each batch ≥ 104 cells/kg body weight, cell viability ≥ 70%, transduction efficiency ≥ 20% and hypomethylation of the FoxP3 gene (Treg-specific demethylated region [TSDR]) ≥ 80%. Other manufacturing variables included Treg identity and maturation by phenotyping, residual bead count, vector copy number, endotoxin level, sterility, and presence of mycoplasma. The characteristics of leukapheresate starting material and drug product from patients with ESRD were compared with those from commercially purchased leukapheresate from 10 healthy donors.

Results
No safety issues were identified during leukapheresis collections. Batches of drug product were manufactured from all 4 patients with ESRD and met the predefined success criteria. There was some variability in leukapheresate starting material in terms of volume of apheresis and total leukocyte counts between patients with ESRD and healthy donors, but percentage differential white blood cell counts were comparable. The quality, quantity and functional activity of manufactured CAR-Tregs were similar between ESRD patients and healthy donors. CAR-Treg drug product from one patient with pre-existing lymphopenia had similar high quality but reduced cell quantity compared with batches from the other patients with ESRD, although yield was still above the predefined target minimum number of cells.

Conclusions
Manufacture of high-quality naïve CAR-Tregs from patients with ESRD is safe and feasible.
Fever in the initial stage of IIM patients: an early clinical warning sign for AE-ILD
Authors: Liu Ting , Chen Haifeng , Shi Yitian , Xu Wei , Yuan Fenghong 
Published: July 2023

Abstract
Background
Fever is a common symptom of Idiopathic inflammatory myopathies (IIM). However, the exact correlation between fever and the prognosis of IIM is still unclear. This study aims to clarify if the IIM patients initiated with fever are associated with poorer outcomes.

Methods
This was a single-center retrospective cohort study. Data were collected from 79 newly diagnosed, treatment-naive IIM patients in the Affiliated Wuxi People’s Hospital of Nanjing Medical University (Wuxi, Jiangsu, China) from November 2016 to June 2020. According to the presence or absence of fever at the onset, the IIM patients were divided into two groups(fever group n = 28, without fever group n = 51) Clinical characteristics, laboratory data, treatment, and outcomes were recorded. The Kaplan-Meier and log-rank tests were used to compare the all-cause mortality, relapse rate, and acute exacerbation of interstitial lung disease (AE-ILD) incidence. The association of fever with the outcomes was assessed in the unadjusted and adjusted forward logistic regression model.

Results
Compared with the non-fever group, the age at onset of the fever group was higher, and mechanic’s hands (MH) and interstitial lung disease (ILD) were more common. Systemic inflammation (CRP and ESR) was significantly higher in the fever group, while the level of albumin(ALB) and muscle enzymes were lower. The fever group seemed to be received more aggressive treatment, with higher dose glucocorticoids and higher rates of intravenous immunoglobulins(IVIG) use. The all-cause mortality rate and the incidence rate of AE-ILD were higher in the fever group. Even adjusted for the age at onset and treatments, fever was significantly associated with AE-ILD and all-cause mortality.

Conclusion
Our study has demonstrated that fever at initial diagnosis is associated with AE-ILD and mortality. Fever should serve as an early clinical warning sign for poor outcomes in IIM patients.
Derivation and validation of a screening tool for stroke-associated sepsis
Authors: Stösser Sebastian , Kleusch Lisa , Schenk Alina , Schmid Matthias , Petzold Gabor C. 
Published: July 2023

Abstract
Background
Post-stroke infections may cause sepsis, which is associated with poor clinical outcome. Sepsis is defined by life-threatening organ dysfunction that can be identified using the Sequential Organ Failure Assessment (SOFA) score. The applicability of the SOFA score for patients not treated on an intensive care unit (ICU) is limited. The aim of this study was to develop and validate an easier-to-use modification of the SOFA score for stroke patients.

Methods
Using a registry-based cohort of 212 patients with large vessel occlusion stroke and infection, potential predictors of a poor outcome indicating sepsis were assessed by logistic regression. The derived score was validated on a separate cohort of 391 patients with ischemic stroke and infection admitted to our hospital over a period of 1.5 years.

Results
The derived Stroke-SOFA (S-SOFA) score included the following predictors: National Institutes of Health stroke scale ≥ 14, peripheral oxygen saturation < 90%, mean arterial pressure < 70 mmHg, thrombocyte count < 150 109/l and creatinine ≥ 1.2 mg/dl. The area under the receiver operating curve for the prediction of a poor outcome indicating sepsis was 0.713 [95% confidence interval: 0.665–0.762] for the S-SOFA score, which was comparable to the standard SOFA score (0.750 [0.703–0.798]), but the prespecified criteria for non-inferiority were not met (p = 0.115). However, the S-SOFA score was non-inferior compared to the SOFA score in non-ICU patients (p = 0.013).

Conclusions
The derived S-SOFA score may be useful to identify non-ICU patients with stroke-associated sepsis who have a high risk of a poor outcome.
Explainable machine learning for hydrocarbon prospect risking
Authors: Mustafa Ahmad , Koster Klaas , AlRegib Ghassan 
Published: July 2023

Hydrocarbon prospect risk assessment is an important process in oil and gas exploration involving the integrated analysis of various geophysical data modalities, including seismic data, well logs, and geologic information, to estimate the likelihood of drilling success for a given drill location. Over the years, geophysicists have attempted to understand the various factors at play influencing the probability of success for hydrocarbon prospects. Toward this end, a large database of prospect drill outcomes and associated attributes has been collected and analyzed via correlation-based techniques to determine the features that contribute the most in deciding the final outcome. Machine learning (ML) has the potential to model complex feature interactions to learn input-output mappings for complicated high-dimensional data sets. However, in many instances, ML models are not interpretable to end users, limiting their utility toward understanding the underlying scientific principles for the problem domain and being deployed to assist in the risk assessment process. In this context, we leverage the concept of explainable ML to interpret various black-box ML models trained on the aforementioned prospect database for risk assessment. Using various case studies on real data, we determine that this model-agnostic explainability analysis for prospect risking can (1) reveal novel scientific insights into the interplay of various features in regard to deciding prospect outcome, (2) assist with performing feature engineering for ML models, (3) detect bias in data sets involving spurious correlations, and (4) build a global picture of a model’s understanding of the data by aggregating local explanations on individual data points.
Three Cases of Non-islet Cell Tumor Hypoglycemia Highlighting Efficacy of Glucocorticoid Treatment
Authors: Voon Kimberly , Simpson Aaron , Fegan Peter Gerard , Walsh John P 
Published: July 2023

Abstract
Non-islet cell tumor hypoglycemia (NICTH) is a rarely encountered cause of hypoglycemia. It is most often caused by tumor secretion of precursor insulin-like growth factor-2 (IGF-2) which, in high concentrations, binds to insulin receptors exerting insulin-like metabolic effects. It is often associated with mesenchymal and hepatic tumors. We describe 3 cases of NICTH: a 60-year-old man with an unresectable pelvic sarcoma and two women ages 43 and 57 with metastatic hemangiopericytoma. Biochemical assessment identified hypoglycemia associated with suppressed insulin, c-peptide, and beta-hydroxybutyrate levels. Each patient was treated with oral glucocorticoids, which effectively prevented recurrence of hypoglycemia and this effect was sustained long-term. These cases highlight a rarely encountered but important cause of hypoglycemia and demonstrate the long-term efficacy of glucocorticoid treatment in preventing hypoglycemia in cases of NICTH related to surgically unresectable tumors.
Mechanomyography as a Surgical Adjunct for Treatment of Chronic Entrapment Neuropathy: A Case Series
Authors: Javeed Saad , Birenbaum Nathan , Xu Yameng , Dibble Christopher F. , Greenberg Jacob K. , Zhang Justin K. , Benedict Braeden , Sydnor Kiersten , Dy Christopher J. , Brogan David M. , Faraji Amir H. , Spinner Robert J. , Ray Wilson Z. 
Published: July 2023

BACKGROUND:
Chronic entrapment neuropathy results in a clinical syndrome ranging from mild pain to debilitating atrophy. There remains a lack of objective metrics that quantify nerve dysfunction and guide surgical decision-making. Mechanomyography (MMG) reflects mechanical motor activity after stimulation of neuromuscular tissue and may indicate underlying nerve dysfunction.

OBJECTIVE:
To evaluate the role of MMG as a surgical adjunct in treating chronic entrapment neuropathies.

METHODS:
Patients 18 years or older with cubital tunnel syndrome (n = 8) and common peroneal neuropathy (n = 15) were enrolled. Surgical decompression of entrapped nerves was performed with intraoperative MMG of the hypothenar and tibialis anterior muscles. MMG stimulus thresholds (MMG-st) were correlated with compound muscle action potential (CMAP), motor nerve conduction velocity, baseline functional status, and clinical outcomes.

RESULTS:
After nerve decompression, MMG-st significantly reduced, the mean reduction of 0.5 mA (95% CI: 0.3-0.7, P < .001). On bivariate analysis, MMG-st exhibited significant negative correlation with common peroneal nerve CMAP (P < .05), but no association with ulnar nerve CMAP and motor nerve conduction velocity. On preoperative electrodiagnosis, 60% of nerves had axonal loss and 40% had conduction block. The MMG-st was higher in the nerves with axonal loss as compared with the nerves with conduction block. MMG-st was negatively correlated with preoperative hand strength (grip/pinch) and foot-dorsiflexion/toe-extension strength (P < .05). At the final visit, MMG-st significantly correlated with pain, PROMIS-10 physical function, and Oswestry Disability Index (P < .05).

CONCLUSION:
MMG-st may serve as a surgical adjunct indicating axonal integrity in chronic entrapment neuropathies which may aid in clinical decision-making and prognostication of functional outcomes.
Deletion of taf1 and taf5 in zebrafish capitulate cardiac and craniofacial abnormalities associated with TAFopathies through perturbations in metabolism
Authors: Leid Jamison , Gray Ryan , Rakita Peter , Koenig Andrew L. , Tripathy Rohan , Fitzpatrick James A. J. , Kaufman Charles , Solnica-Krezel Lilianna , Lavine Kory J. 
Published: July 2023

ABSTRACT
Intellectual disability is a neurodevelopmental disorder that affects 2-3% of the general population. Syndromic forms of intellectual disability frequently have a genetic basis and are often accompanied by additional developmental anomalies. Pathogenic variants in components of TATA-binding protein associated factors (TAFs) have recently been identified in a subset of patients with intellectual disability, craniofacial hypoplasia, and congenital heart disease. This syndrome has been termed as a TAFopathy and includes mutations in TATA binding protein (TBP), TAF1, TAF2, and TAF6. The underlying mechanism by which TAFopathies give rise to neurodevelopmental, craniofacial, and cardiac abnormalities remains to be defined. Through a forward genetic screen in zebrafish, we have recovered a recessive mutant phenotype characterized by craniofacial hypoplasia, ventricular hypoplasia, heart failure at 96 h post-fertilization and lethality, and show it is caused by a nonsense mutation in taf5. CRISPR/CAS9 mediated gene editing revealed that these defects where phenocopied by mutations in taf1 and taf5. Mechanistically, taf5-/- zebrafish displayed misregulation in metabolic gene expression and metabolism as evidenced by RNA sequencing, respiration assays, and metabolite studies. Collectively, these findings suggest that the TAF complex may contribute to neurologic, craniofacial, and cardiac development through regulation of metabolism.
Innervation of the developing kidney in vivo and in vitro
Authors: Tarnick Julia , Elhendawi Mona , Holland Ian , Chang Ziyuan , Davies Jamie A. 
Published: July 2023

ABSTRACT
Within the adult kidney, renal neurites can be observed alongside the arteries where they play a role in regulating blood flow. However, their role and localization during development has so far not been described in detail. In other tissues, such as the skin of developing limb buds, neurons play an important role during arterial differentiation. Here, we aim to investigate whether renal nerves could potentially carry out a similar role during arterial development in the mouse kidney. In order to do so, we used whole-mount immunofluorescence staining to identify whether the timing of neuronal innervation correlates with the recruitment of arterial smooth muscle cells. Our results show that neurites innervate the kidney between day 13.5 and 14.5 of development, arriving after the recruitment of smooth muscle actin-positive cells to the renal arteries.