syedzayyan/paper_mill_benchmark huggingface dataset:
Rectal screening for azole non-susceptible Candida species in patients undergoing liver transplantation.

Introduction candidiasis is the most common invasive fungal infection in solid organ transplant recipients, and liver transplant (lt) recipients are at heightened risk.We hypothesized that pre-transplant screening for azole non-susceptible candida (ansc) allows for tailored antifungal prophylaxis to reduce the incidence of post-lt ansc infection.Methods we performed a retrospective chart review of adult (age ≥18 years) patients who underwent lt at yale new haven hospital from april 2019 to march 2021.Screening for ansc, defined as candida glabrata or candida krusei, was performed using a rectal swab prior to or at the time of lt.Results during the study period, ansc screening was performed in 47 patients who underwent a total of 48 lts, with 46/48 (96%) primary lts and two re-transplantations.Ten of 48 screened cases (21%) had ansc-positive rectal swabs.Only seven of 10 ansc-colonized patients received appropriate antifungal prophylaxis (i.e., anidulafungin), and one of these seven patients developed candidemia within 30 days of lt.The median number of candidiasis risk factors was one, and 29% of the cohort had two or more risk factors.Discussion routine ansc screening of lt candidates may assist in selecting appropriate antifungal prophylaxis but may be insufficient to prevent infection in those with multiple risk factors for candida infection.

Journal: Transplant infectious disease : an official journal of the Transplantation Society (2022)
Publication types: Journal Article
Performance and Enhancement of Various Fillers Guiding Vanadium (V) Bioremediation.

Bioremediation of vanadium (v) pollution in groundwater is an emerging topic.However, knowledge of v in a biogeochemical process is limited and long-term effective removal methods are lacking.V(v) remediation processes by various kinds of auxiliary fillers (maifanite-1, maifanite-2, volcanic rock, green zeolite and ceramsite), agricultural biomass and microbial enhancing were explored in this study.In tests without inocula, the v(v) removal efficiencies of ceramsite (inert filler) and maifanite-2 (active filler) were 84.9% and 60.5%, respectively.When inoculated with anaerobic sludge, 99.9% of v(v) could be removed with the synergistic performance of straw and maifanite-2.Toc (total organic carbon), trace elements and three-dimensional fluorescence analyses confirmed that maifanite-2 was the most suitable among various fillers in biological v(v) removal systems with straw.This study provides a collaborative method (adsorption-biology) by using straw with maifanite-2 in v(v)-contaminated groundwater.The knowledge gained in this study will help develop permeable reactive barrier technology to repair polluted groundwater to put forward a reasonable, effective and sustainable environmental treatment strategy.

Journal: International journal of environmental research and public health (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
CRISPR-Cas9 In Vivo Gene Editing for Transthyretin Amyloidosis.

Transthyretin amyloidosis, also called attr amyloidosis, is a life-threatening disease characterized by progressive accumulation of misfolded transthyretin (ttr) protein in tissues, predominantly the nerves and heart.Ntla-2001 is an in vivo gene-editing therapeutic agent that is designed to treat attr amyloidosis by reducing the concentration of ttr in serum.It is based on the clustered regularly interspaced short palindromic repeats and associated cas9 endonuclease (crispr-cas9) system and comprises a lipid nanoparticle encapsulating messenger rna for cas9 protein and a single guide rna targeting ttr.Methods after conducting preclinical in vitro and in vivo studies, we evaluated the safety and pharmacodynamic effects of single escalating doses of ntla-2001 in six patients with hereditary attr amyloidosis with polyneuropathy, three in each of the two initial dose groups (0.1 mg per kilogram and 0.3 mg per kilogram), within an ongoing phase 1 clinical study.Results preclinical studies showed durable knockout of ttrafter a single dose.Serial assessments of safety during the first 28 days after infusion in patients revealed few adverse events, and those that did occur were mild in grade.Dose-dependent pharmacodynamic effects were observed.At day 28, the mean reduction from baseline in serum ttr protein concentration was 52% (range, 47 to 56) in the group that received a dose of 0.1 mg per kilogram and was 87% (range, 80 to 96) in the group that received a dose of 0.3 mg per kilogram.Conclusions in a small group of patients with hereditary attr amyloidosis with polyneuropathy, administration of ntla-2001 was associated with only mild adverse events and led to decreases in serum ttr protein concentrations through targeted knockout of ttr.(funded by intellia therapeutics and regeneron pharmaceuticals; clinical trials.gov number, nct04601051.).

Journal: The New England journal of medicine (2021)
Publication types: Clinical Trial, Phase I;Journal Article;Multicenter Study;Research Support, Non-U.S. Gov't
A proposed framework for point of care lung ultrasound by respiratory physiotherapists: scope of practice, education and governance.

Point of care ultrasound (po cus) has the potential to provide a step change in the management of patients across a range of healthcare settings.Increasingly, healthcare practitioners who are not medical doctors are incorporating po cus into their clinical practice.However, the professional, educational and regulatory environment in which this occurs is poorly developed, leaving clinicians, managers and patients at risk.Main body drawing upon existing medical and non-medical literature, the authors present a proposed framework for the use of po cus.Throughout, mechanisms for applying the principles to other professionals and healthcare settings are signposted.Application of the framework is illustrated via one such group of healthcare practitioners and in a particular healthcare setting: respiratory physiotherapists in the uk.In defining the point of care lus scope of practice we detail what structures are imaged, differentials reported upon and clinical decisions informed by their imaging.This is used to outline the educational and competency requirements for respiratory physiotherapists to safely and effectively use the modality.Together, these are aligned with the regulatory (professional, legal and insurance) arrangements for this professional group in the uk.In so doing, a comprehensive approach for respiratory physiotherapists to consolidate and expand their use of point of care lus is presented.This provides clarity for clinicians as to the boundaries of their practice and how to train in the modality; it supports educators with the design of courses and alignment of competency assessments; it supports managers with the staffing of existing and new care pathways.Ultimately it provides greater accessibility for patients to safe and effective point of care lung ultrasound.For clinicians who are not respiratory physiotherapists and/or are not based in the uk, the framework can be adapted to other professional groups using point of care lus as well as other point of care ultrasound (po cus) applications, thereby providing a comprehensive and sustainable foundation for po cus consolidation and expansion.Conclusion this paper presents a comprehensive framework to support the use of point of care lus by respiratory physiotherapists in the uk.Mechanisms to adapt the model to support a wide range of other po cus users are outlined.

Journal: The ultrasound journal (2022)
Publication types: Journal Article;Review
Bandage contact lens use after photorefractive keratectomy.

The use of a bandage contact lens (bcl) immediately after photorefractive keratectomy (prk) results in less pain.This review analyzed which bcl is most effective in decreasing pain immediately after prk and evaluated the reepithelialization process in the treated zone.Two databases, pub med and medline, were checked for articles published from january 2005 to may 2018.The keywords were photorefractive keratectomy, prk, contact lens, and bandage contact lens.The review comprised 13 studies; these studies enrolled 842 patients who had prk.All studies compared the early postoperative results for two types of bcl material (senofilcon a and lotrafilcon a).Of the materials, the pain scores were lowest with a senofilcon a.The size of the defect in the epithelialized area 1 day after surgery decreased fastest with lotrafilcon a.

Journal: Journal of cataract and refractive surgery (2019)
Publication types: Journal Article;Review
Cell-Derived Extracellular Matrix for Tissue Engineering and Regenerative Medicine.

Cell-derived extracellular matrices (cd-ecms) captured increasing attention since the first studies in the 1980s.The biological resemblance of cd-ecms to theirin vivocounterparts and natural complexity provide them with a prevailing bioactivity.Cd-ecms offer the opportunity to produce microenvironments with costumizable biological and biophysical properties in a controlled setting.As a result, cd-ecms can improve cellular functions such as stemness or be employed as a platform to study cellular niches in health and disease.Either on their own or integrated with other materials, cd-ecms can also be utilized as biomaterials to engineer tissuesde novoor facilitate endogenous healing and regeneration.This review provides a brief overview over the methodologies used to facilitate cd-ecm deposition and manufacturing.It explores the versatile uses of cd-ecm in fundamental research and therapeutic approaches, while highlighting innovative strategies.Furthermore, current challenges are identified and it is accentuated that advancements in methodologies, as well as innovative interdisciplinary approaches are needed to take cd-ecm-based research to the next level.

Journal: Frontiers in bioengineering and biotechnology (2020)
Publication types: Journal Article;Review
North American Study for the Treatment of Recurrent Epistaxis with Doxycycline: The NOSTRIL trial.

Hereditary hemorrhagic telangiectasia (hht) is a vascular bleeding disorder characterized by mucocutaneous telangiectasias and visceral arteriovenous malformations.A frequently debilitating symptom is spontaneous recurrent epistaxis.Objective to evaluate whether doxycycline therapy improves epistaxis in hht by using a prospective, randomized, placebo-controlled crossover study design.Patients/methods twenty-two eligible patients between december 2017 and july 2020 at a single center were randomized to one of two study arms: doxycycline treatment followed by placebo, or vice versa.Primary outcomes measured differences in epistaxis severity between treatments.Changes in quality of life, laboratory markers of bleeding, and number of monthly blood transfusions or iron infusions were assessed as secondary endpoints.Additional post hoc endpoints included frequency and duration of dripping epistaxis and gushing epistaxis.A post hoc longitudinal analysis assessed effects of doxycycline over time.Results/conclusions doxycycline was safe and well tolerated.However, there was no reduction in the three primary outcome measures, nosebleed frequency (p = .16), nosebleed duration (p = .05), and epistaxis severity score (p = .19).Quality of life, hemoglobin level, and number of blood transfusions and iron infusions did not differ between groups.Post hoc analysis demonstrated reduction in instances of gushing (p = .02) with doxycycline, although this finding is of unclear clinical significance.Post hoc longitudinal analysis showed reduction in frequency (mean estimate of coefficient = -0.19, standard error = 0.07, p = .01) and duration (mean estimate of coefficient = -2.33, standard error = 1.08, p = .03) of epistaxis over time.Post hoc findings suggest possible benefit of doxycycline but should be interpreted with caution given the overall negative study.Further investigation is needed with a larger sample size and a longer treatment duration.

Journal: Journal of thrombosis and haemostasis : JTH (2022)
Publication types: Journal Article;Randomized Controlled Trial;Research Support, Non-U.S. Gov't
Visual Outcomes After Treatment for Sporadic Optic Pathway Gliomas in Pediatric Patients: A Systematic Review.

Optic pathway gliomas (opgs) typically occur in the first decade of life and 40%-50% are not associated with neurofibromatosis 1 (nf1) (sporadic).Management strategies are often patient specific because of the variable and unpredictable course.No study has summarized the effect of treatment strategies on visual outcomes in the subset of pediatric patients with sporadic opg.Methods we conducted a systematic review to determine the nature of visual outcomes in pediatric patients with sporadic, non-nf1-associated opg using the pub med, embase, scopus, cochrane, and cinahl plus databases.Visual outcomes were categorized as improved, unchanged, or deteriorated.Results of 1316 results, 31 articles were included.Treatment indications are unknown with full clinical detail.A total of 45.2% (14/31) reported deteriorated outcomes after treatment, 35.5% (11/31) no change, and 19.4% (6/31) improvement.Of radiotherapy studies, 50.0% (4/8) found no change, 37.5% (3/8) deterioration, and 12.5% (1/8) improvement.Of chemotherapy studies, 35.7% (5/14) each showed improvement and deterioration, whereas 28.6% (4/14) showed no change.Of surgical studies, 62.5% (5/8) indicated deterioration, and 37/5% (3/8) indicated no change.The singular study examining observation reported deterioration in visual outcomes.Factors associated with poor visual outcomes included signs and symptoms of visual decline at presentation, involvement of the intraorbital optic nerve, and intracranial hypertension requiring surgery.Causality cannot be determined from systematic review.Conclusions most studies showed that vision in pediatric patients with sporadic opg is stable to poor after observation, chemotherapy, radiotherapy, or surgery.Chemotherapy may be associated with most favorable visual outcomes.

Journal: World neurosurgery (2022)
Publication types: Journal Article;Review;Systematic Review
Polysaccharide ofAtractylodes macrocephalaKoidz Alleviates Cyclophosphamide-Induced Thymus Ferroptosis in Gosling.

The present study aimed to explore the mechanism by which pamk alleviates cyclophosphamide (ctx)-induced ferroptosis in thymocytes.One-day-old goslings were divided into four groups (10 goslings/group).The con and ctx groups were fed a basic diet.The pamk and ctx + pamk groups were fed the basic diet mixed with pamk (400 mg/kg).Moreover, the ctx and ctx + pamk groups were given a daily injection of 40 mg/kg bw of ctx (at 19, 20, and 21 days of age).On the other hand, the con and pamk groups were given 0.5 m l of sterilized saline into the leg muscle (at 19, 20, and 21 days of age).The goslings were fed for 28 days.The ferroptosis pathway was enriched in transcriptome sequencing.Compared to the con group, the thymus in the ctx group underwent injury, and the mitochondria of thymocytes showed features of ferroptosis.Pamk treatment alleviated ferroptosis in thymocytes and thymus injury, and ctx-induced elevated levels of oxidative stress and iron content restored gpx4 protein expression (p < 0.05) and inhibited the ctx-induced activation of the ferroptosis pathway (p < 0.05).Conclusively, pamk could reduce thymus injury by alleviating ctx-induced thymocyte ferroptosis in gosling to alleviate the immunosuppression caused by ctx in the organism.

Journal: Animals : an open access journal from MDPI (2022)
Publication types: Journal Article
Mini-Open Subpectoral Biceps Tenodesis Using a Suture Anchor with Bone-Bridge Backup.

Pathology of the long head of the biceps tendon is a known cause of anterior shoulder pain.Current surgical management options include tenotomy and tenodesis.Tenodesis can be performed arthroscopically or as an open procedure.Arthroscopic tenodesis typically uses a suprapectoral attachment, which may fail to address tendon pathology in the bicipital groove.Open tenodesis carries iatrogenic risk to neurovascular structures and a fracture risk while drilling, as well as the morbidity of an open procedure.This technique paper describes a mini-open subpectoral approach using a suture anchor and bone bridge backup for dual fixation.Use of a suture anchor instead of an interference screw reduces drill hole diameter reducing the risk of iatrogenic humeral fracture.Dual fixation provides a robust repair which may be of use for athletic patients desiring an accelerated recovery.

Journal: Arthroscopy techniques (2021)
Publication types: Journal Article
The feasibility of improving discourse in people with aphasia through AAC: Clinical and functional MRI correlates.

S the purpose of this study is twofold: (1) to examine the feasibility of providing high-tech augmentative and alternative communication (aac) treatment to people with chronic aphasia, with the goal of evoking changes in spoken language; and (2) to identify evidence of aac-induced changes in brain activation.Method & procedures we employed a pre- post-treatment design with a control (usual care) group to observe the impact of an aac treatment on aphasia severity and spoken discourse.Further, we used functional magnetic resonance imaging (f mri) to examine associated neural reorganization.Outcomes & results compared to the usual care group, the aac intervention trended toward larger treatment effects and resulted in a higher number of responders on behavioral outcomes.Both groups demonstrated a trend toward greater leftward lateralization of language functions via f mri.Secondary analyses of responders to treatment revealed increased activation in visual processing regions, primarily for the aac group.Conclusions this study provides preliminary guidance regarding how to implement aac treatment in a manner that simultaneously facilitates language recovery across a variety of aphasia types and severity levels while compensating for residual deficits in people with chronic aphasia.Further, this work motivates continued efforts to unveil the role of aac-based interventions in the aphasia recovery process and provides insight regarding the neurobiological mechanisms supporting aac-induced language changes.

Journal: Aphasiology (2018)
Publication types: Journal Article
Early Noise-Induced Hearing Loss Accelerates Presbycusis Altering Aging Processes in the Cochlea.

Several studies identified hearing loss as a risk factor for aging-related processes, including neurodegenerative diseases, as dementia and age-related hearing loss (arhl).Although the association between hearing impairment in midlife and arhl has been widely documented by epidemiological and experimental studies, the molecular mechanisms underlying this association are not fully understood.In this study, we used an established animal model of arhl (c57bl/6 mice) to evaluate if early noise-induced hearing loss (nihl) could affect the onset or progression of age-related cochlear dysfunction.We found that hearing loss can exacerbate arhl, damaging sensory-neural cochlear epithelium and causing synaptopathy.Moreover, we studied common pathological markers shared between hearing loss and arhl, demonstrating that noise exposure can worsen/accelerate redox status imbalance [increase of reactive oxygen species (ros) production, lipid peroxidation, and dysregulation of endogenous antioxidant response] and vascular dysfunction [increased expression of hypoxia-inducible factor-1alpha (hif-1α) and vascular endothelial growth factor c (vegfc)] in the cochlea.Unveiling the molecular mechanisms underlying the link between hearing loss and aging processes could be valuable to identify effective therapeutic strategies to limit the effect of environmental risk factors on age-related diseases.

Journal: Frontiers in aging neuroscience (2022)
Publication types: Journal Article
Perspective on therapeutic and diagnostic potential of camel nanobodies for coronavirus disease-19 (COVID-19).

In this paper, we focus on the camelid nanobodies as a revolutionary therapy that can guide efforts to discover new drugs for coronavirus disease (covid-19).The small size property makes nanobodies capable of penetrating efficiently into tissues and recognizing cryptic antigens.Strong antigen affinity and stability in the gastrointestinal tract allow them to be used via oral administration.In fact, the use of nanobodies as inhalant can be directly delivered to the target organ, conferring high pulmonary drug concentrations and low systemic drug concentrations and minimal systemic side effects.For that, nanobodies are referred as a class of next-generation antibodies.Nanobodies permit the construction of multivalent formats that may achieve ultra-high neutralization potency and then may prevent mutational escape and can neutralize a wide range of sars-co v-2 variants.Due to their distinctive characteristics, nanobodies can be of great use in the development of promising treatment or preventive strategies against sars-co v-2 infection.In this review, the state-of-the-art of camel nanobodies design strategies against the virus including sars-co v-2 are critically summarized.The application of general nanotechnology was also discussed to mitigate and control emerging sars-co v-2 infection.

Journal: 3 Biotech (2021)
Publication types: Journal Article;Review
Impact of biosurfactant and iron nanoparticles on biodegradation of polyaromatic hydrocarbons (PAHs).

Polycyclic aromatic hydrocarbons (pahs) are hazardous toxic contaminants and considered as primary pollutants due to their persistent nature and most of them are carcinogenic and mutagenic.The key challenge in pahs degradation is their hydrophobic nature, which makes them one of the most complex materials and inaccessible by a broad range of microorganisms.This bioavailability can be increased by using a biosurfactant.In the present study mixed pahs were degraded using the biosurfactant producing bacterial strains.In addition, iron nanoparticles were synthesized and the impact of iron nanoparticles on the growth of the mixed bacterial strains (pseudomonas stutzeri na3 and acinetobacter baumannii mn3) was optimized.The mixed pahs (anthracene, pyrene, and benzo(a)pyrene) degradation was enhanced by addition of biosurfactant (produced by bacillus subtilis a1) and iron nanoparticles, resulting in 85% of degradation efficiency.The addition of the biosurfactant increased the bioavailability of the pahs in the aqueous environment, which might help bacterial cells for the initial settlement and development.The addition of iron nanoparticles increased both bacterial biomass and pahs adsorption over their surface.These overall interactions assisted in the utilization of pahs by the mixed bacterial consortia.This study illustrates that this integrated approach can be elaborated for the removal of the complex pahs pollutants from soil and aqueous environments.

Journal: Environmental pollution (Barking, Essex : 1987) (2022)
Publication types: Journal Article