bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted sequencing analysis pipeline for species identification of human pathogenic fungi using long-read nanopore sequencing
Authors: Langsiri Nattapong , Worasilchai Navaporn , Irinyi Laszlo , Jenjaroenpun Piroon , Wongsurawat Thidathip , Luangsa-ard Janet Jennifer , Meyer Wieland , Chindamporn Ariya 
Published: September 2023

AbstractAmong molecular-based techniques for fungal identification, Sanger sequencing of the primary universal fungal DNA barcode, the internal transcribed spacer (ITS) region (ITS1, 5.8S, ITS2), is commonly used in clinical routine laboratories due to its simplicity, universality, efficacy, and affordability for fungal species identification. However, Sanger sequencing fails to identify mixed ITS sequences in the case of mixed infections. To overcome this limitation, different high-throughput sequencing technologies have been explored. The nanopore-based technology is now one of the most promising long-read sequencing technologies on the market as it has the potential to sequence the full-length ITS region in a single read. In this study, we established a workflow for species identification using the sequences of the entire ITS region generated by nanopore sequencing of both pure yeast isolates and mocked mixed species reads generated with different scenarios. The species used in this study included Candida albicans (n = 2), Candida tropicalis (n = 1), Nakaseomyces glabratus (formerly Candida glabrata) (n = 1), Trichosporon asahii (n = 2), Pichia kudriavzevii (formerly Candida krusei) (n = 1), and Cryptococcus neoformans (n = 1). Comparing various methods to generate the consensus sequence for fungal species identification, the results from this study indicate that read clustering using a modified version of the NanoCLUST pipeline is more sensitive than Canu or VSEARCH, as it classified species accurately with a lower abundance cluster of reads (3% abundance compared to 10% with VSEARCH). The modified NanoCLUST also reduced the number of classified clusters compared to VSEARCH, making the subsequent BLAST+ analysis faster. Subsampling of the datasets, which reduces the size of the datasets by approximately tenfold, did not significantly affect the identification results in terms of the identified species name, percent identity, query coverage, percentage of reads in the classified cluster, and the number of clusters. The ability of the method to distinguish mixed species within sub-populations of large datasets has the potential to aid computer analysis by reducing the required processing power. The herein presented new sequence analysis pipeline will facilitate better interpretation of fungal sequence data for species identification.
Immune boosting functional components of natural foods and its health benefits
Authors: Stephen Jaspin , Manoharan Dharini , Radhakrishnan Mahendran 
Published: September 2023

AbstractNaturally available foods contain nutrients like vitamins (A, C, E, and D), zinc, calcium, magnesium, folate iron, omega fatty acids, selenium, and phytochemicals that have profound protective effects (boosting immunity) on human from diseases. The critical component of obtaining incredible health is to maintain proper diet with healthy food, proper sleep, and regular exercise. This review is drafted with an aim to lay out the importance of consuming immune boosting foods, present various nutritional compounds available and their mechanism in maintaining immunity, and briefly discuss some of the exotic immunity building food sources, nutrients present, health benefits, and its utilization. Some of the immune-boosting foods like almonds, spinach, citrus fruits, avocado, red bell pepper, pomegranate, kiwi, garlic, ginger, and passion fruit are deliberated to have positive impact on ameliorating cancer, diabetics, heart disease, skin, eyesight, bone health, blood pressure, brain development, anti-stress, antimicrobial, antibacterial, antifungal, anti-aging, anti-allergenicity, antimalarial, anti-mutagenicity, and anti-inflammatory. This review on immune boosting foods further emphasizes on the need and proved the importance of consuming natural fruits, vegetables, nut, and meat products for strengthening the immune system. Thus, the consumption of immune boosting foods is mandatory for maintaining the health and protecting our body from harmful pathogen and degenerative diseases naturally.Novelty impact statementExploring diet-health approach is very important in the domain of food for enhancing immune response and activation in humans. Natural food that has health and nutritional benefits has made a noteworthy influence on changing consumer's lifestyles. The immune-strengthening foods with proper dietary recommendation play a significant role to increase the immunity of people.
Graphical Abstract
Acute bilateral renal infarction after left upper pulmonary lobectomy: a case report
Authors: Matsuzaki Tomohiko , Matsuo Kazuhiro , Higeta Tomoki , Shioyama Kie , Nakano Kei , Onozawa Hiroto , Tsuboi Takaaki , Hashimoto Ryo , Wada Atsushi , Aruga Naohiro , Masuda Ryota , Iwazaki Masayuki 
Published: September 2023

Abstract
Background
Left upper lobectomy (LUL) is considered a risk factor for thrombus formation in the pulmonary vein stump compared with other lobectomies, and it occurs in 11.7–13.5% of cases. Although cerebral infarction after LUL has been reported in many articles, reports of bilateral renal infarction after lobectomy are rare.

Case presentation
A 70-year-old male patient was admitted to our hospital with a diagnosis of lung cancer. The nodule’s diameter was 2.5 cm on computed tomography, and it was diagnosed as a non-small cell lung carcinoma by a bronchoscopic biopsy. The clinical stage was cT1c N0M0 (c-stageIA3). The patient underwent thoracoscopic LUL and systemic lymph node dissection. No complications were observed during the operation, and the immediate postoperative period was uneventful until postoperative day 3. On postoperative day 4, he experienced fever, abdominal pain, and nausea, which spontaneously resolved. Laboratory data showed an elevated white blood cell count, and elevated serum lactate dehydrogenase and creatinine concentrations. Contrast-enhanced computed tomography from the thorax to the pelvic cavity showed a partial defect of the bilateral kidneys. We diagnosed the patient with bilateral renal infarction.

Conclusions
Bilateral renal infarction after lobectomy is a rare and serious condition, which should be diagnosed as early as possible. Since all cases of reported renal infarctions occurred after LUL, special attention should be paid to postoperative management after performing LUL.
A tool for safer prescribing in vulnerable adults: the continuing development of the Medichec app and website
Authors: Bishara Delia , Riaz Sahar , Sauer Justin , Mueller Christoph , Gee Siobhan , Taylor David , Wilcha Robyn-Jenia , Edwards Millie , Beehuspoteea Nirja , Mallia Anne Marie Bonnici , Brook Jennifer , Balasundaram Bharathi , Harwood Daniel , Funnell Nicola , Strydom Andre , Stewart Robert 
Published: September 2023

Aims and methodAdverse effects are a common concern when prescribing and reviewing medication, particularly in vulnerable adults such as older people and those with intellectual disability. This paper describes the development of an app giving information on side-effects, called Medichec, and provides a description of the processes involved in its development and how drugs were rated for each side-effect. Medications with central anticholinergic action, dizziness, drowsiness, hyponatraemia, QTc prolongation, bleeding and constipation were identified using the British National Formulary (BNF) and frequency of occurrence of these effects was determined using the BNF, product information and electronic searches, including PubMed.ResultsMedications were rated using a traffic light system according to how commonly the adverse effect was known to occur or the severity of the effect.Clinical implicationsMedichec can facilitate access to side-effects information for multiple medications, aid clinical decision-making, optimise treatment and improve patient safety in vulnerable adults.
Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes
Authors: Parker Joel S. , Mullins Michael , Cheang Maggie C.U. , Leung Samuel , Voduc David , Vickery Tammi , Davies Sherri , Fauron Christiane , He Xiaping , Hu Zhiyuan , Quackenbush John F. , Stijleman Inge J. , Palazzo Juan , Marron J.S. , Nobel Andrew B. , Mardis Elaine , Nielsen Torsten O. , Ellis Matthew J. , Perou Charles M. , Bernard Philip S. 
Published: September 2023

PURPOSE To improve on current standards for breast cancer prognosis and prediction of chemotherapy benefit by developing a risk model that incorporates the gene expression–based “intrinsic” subtypes luminal A, luminal B, HER2-enriched, and basal-like. METHODS A 50-gene subtype predictor was developed using microarray and quantitative reverse transcriptase polymerase chain reaction data from 189 prototype samples. Test sets from 761 patients (no systemic therapy) were evaluated for prognosis, and 133 patients were evaluated for prediction of pathologic complete response (pCR) to a taxane and anthracycline regimen. RESULTS The intrinsic subtypes as discrete entities showed prognostic significance ( P = 2.26E-12) and remained significant in multivariable analyses that incorporated standard parameters (estrogen receptor status, histologic grade, tumor size, and node status). A prognostic model for node-negative breast cancer was built using intrinsic subtype and clinical information. The C-index estimate for the combined model (subtype and tumor size) was a significant improvement on either the clinicopathologic model or subtype model alone. The intrinsic subtype model predicted neoadjuvant chemotherapy efficacy with a negative predictive value for pCR of 97%. CONCLUSION Diagnosis by intrinsic subtype adds significant prognostic and predictive information to standard parameters for patients with breast cancer. The prognostic properties of the continuous risk score will be of value for the management of node-negative breast cancers. The subtypes and risk score can also be used to assess the likelihood of efficacy from neoadjuvant chemotherapy.
Mechanism-Based Modeling of Perioperative Variations in Hemoglobin Concentration in Patients Undergoing Laparoscopic Surgery
Authors: Jaramillo Sebastian , Marco-Ariño Nicolás , Montane-Muntane Mar , Blasi Annabel , Navarro-Ripoll Ricard , de Peray-Bruel Claudia , Vila-Cullell Isabel , Gambús Pedro L. , Troconiz Iñaki F. 
Published: September 2023

BACKGROUND:
Hemoglobin concentration ([Hb]) in the perioperative setting should be interpreted in the context of the variables and processes that may affect it to differentiate the dilution effects caused by changes in intravascular volume. However, it is unclear what variables and processes affect [Hb]. Here, we modeled the perioperative variations in [Hb] to identify the variables and processes that govern [Hb] and to describe their effects.

METHODS:
We first constructed a mechanistic framework based on the main variables and processes related to the perioperative [Hb] variations. We then prospectively studied patients undergoing laparoscopic surgery, divided into 2 consecutive cohorts for the development and validation of the model. The study protocol consisted of serial measurements of [Hb] along with recordings of hemoglobin mass loss, blood volume loss, fluid infusion, urine volume, and inflammatory biomarkers measurements, up to 96 hours postoperatively. Mathematical fitting was performed using nonlinear mixed-effects. Additionally, we performed simulations to explore the effects of blood loss and fluid therapy protocols on [Hb].

RESULTS:
We studied 154 patients: 118 enrolled in the development group and 36 in the validation group. We characterized the perioperative course of [Hb] using a mass balance model that accounted for hemoglobin losses during surgery, and a 2-compartment model that estimated fluid kinetics and intravascular volume changes. During model development, we found that urinary fluid elimination represented only 24% of the total fluid elimination, and that total fluid elimination was inhibited after surgery in a time-dependent manner and influenced by age. Also, covariate evaluation showed a significant association between the type of surgery and proportion of fluid eliminated via urine. In contrast, neither the type of infused solution, blood volume loss nor inflammatory biomarkers were found to correlate with model parameters. In the validation analysis, the model demonstrated a considerable predictive capacity, with 95% of the predicted [Hb] within −4.4 and +5.5 g/L. Simulations demonstrated that hemoglobin mass loss determined most of the postoperative changes in [Hb], while intravascular volume changes due to fluid infusion, distribution, and elimination induced smaller but clinically relevant variations. Simulated patients receiving standard fluid therapy protocols exhibited a hemodilution effect that resulted in a [Hb] decrease between 7 and 15 g/L at the end of surgery, and which was responsible for the lowest [Hb] value during the perioperative period.

CONCLUSIONS:
Our model provides a mechanistic and quantitative understanding of the causes underlying the perioperative [Hb] variations.
IL-33 regulates Müller cell-mediated retinal inflammation and neurodegeneration in diabetic retinopathy
Authors: Augustine Josy , Pavlou Sofia , Harkin Kevin , Stitt Alan W. , Xu Heping , Chen Mei 
Published: September 2023

ABSTRACT
Diabetic retinopathy (DR) is characterised by dysfunction of the retinal neurovascular unit, leading to visual impairment and blindness. Müller cells are key components of the retinal neurovascular unit and diabetes has a detrimental impact on these glial cells, triggering progressive neurovascular pathology of DR. Amongst many factors expressed by Müller cells, interleukin-33 (IL-33) has an established immunomodulatory role, and we investigated the role of endogenous IL-33 in DR. The expression of IL-33 in Müller cells increased during diabetes. Wild-type and Il33−/− mice developed equivalent levels of hyperglycaemia and weight loss following streptozotocin-induced diabetes. Electroretinogram a- and b-wave amplitudes, neuroretina thickness, and the numbers of cone photoreceptors and ganglion cells were significantly reduced in Il33−/− diabetic mice compared with those in wild-type counterparts. The Il33−/− diabetic retina also exhibited microglial activation, sustained gliosis, and upregulation of pro-inflammatory cytokines and neurotrophins. Primary Müller cells from Il33−/− mice expressed significantly lower levels of neurotransmitter-related genes (Glul and Slc1a3) and neurotrophin genes (Cntf, Lif, Igf1 and Ngf) under high-glucose conditions. Our results suggest that deletion of IL-33 promotes inflammation and neurodegeneration in DR, and that this cytokine is critical for regulation of glutamate metabolism, neurotransmitter recycling and neurotrophin secretion by Müller cells.
Dynamic gap crossing in Dendrelaphis, the sister taxon of flying snakes
Authors: Graham Mal , Socha John J. 
Published: September 2023

ABSTRACT
Arboreal animals commonly use dynamic gap-crossing behaviors such as jumping. In snakes, however, most species studied to date only employ the quasi-static cantilever crawl, which involves a whole-body reach. One exception is the paradise tree snake (Chrysopelea paradisi), which exhibits kinematic changes as gap distance increases, culminating in dynamic behaviors that are kinematically indistinguishable from those used to launch glides. Because Chrysopelea uses dynamic behaviors when bridging gaps without gliding, we hypothesized that such dynamic behaviors evolved ancestrally to Chrysopelea. To test this predicted occurrence of dynamic behaviors in closely related taxa, we studied gap bridging locomotion in the genus Dendrelaphis, which is the sister lineage of Chysopelea. We recorded 20 snakes from two species (D. punctulatus and D. calligastra) crossing gaps of increasing size, and analyzed their 3D kinematics. We found that, like C. paradisi, both species of Dendrelaphis modulate their use of dynamic behaviors in response to gap distance, but Dendrelaphis exhibit greater inter-individual variation. Although all three species displayed the use of looped movements, the highly stereotyped J-loop movement of Chrysopelea was not observed in Dendrelaphis. These results support the hypothesis that Chrysopelea may have co-opted and refined an ancestral behavior for crossing gaps for the novel function of launching a glide. Overall, these data demonstrate the importance of gap distance in governing behavior and kinematics during arboreal gap crossing.
Hip Pain in an Athlete
Authors: Covey Carlton J. , Knobloch Alexander C. , Kim Alexander R. 
Published: September 2023

Abstract
Hip pain is a common complaint in sports, and narrowing the differential diagnosis can be difficult. Many etiologies are secondary to overuse and respond well to nonsurgical treatment. The increased use of point-of-care ultrasound has helped provide timely and accurate diagnoses and some guided treatments. The hip is in close proximity to the abdomen and pelvis, and clinicians should be familiar with nonmusculoskeletal pain generators. This article is a comprehensive review of hip pain etiologies in athletes.
Commitment Against Front-Running Attacks
Authors: Canidio Andrea , Danos Vincent 
Published: September 2023

We provide a game-theoretic analysis of the problem of front-running attacks. We use it to distinguish attacks from legitimate competition among honest users for having their transactions included earlier in the block. We also use it to introduce an intuitive notion of the severity of front-running attacks. We then study a simple commit-reveal protocol and discuss its properties. This protocol has costs because it requires two messages and imposes a delay. However, we show that it prevents the most severe front-running attacks while preserving legitimate competition between users, guaranteeing that the earliest transaction in a block belongs to the honest user who values it the most. When the protocol does not fully eliminate attacks, it nonetheless benefits honest users because it reduces competition among attackers (and overall expenditure by attackers). This paper was accepted by Joshua Gans, business strategy. Funding: The authors gratefully acknowledge the financial support of the Ethereum Foundation [Grant FY22-0840].
Estratégia democrático-popular e cultura profissional renovada: revisitando os fundamentos do Projeto Ético-Político
Authors: De Sousa Adrianyce A. Silva de Sousa 
Published: September 2023

O presente artigo analisa os fundamentos ídeo-políticos e teórico-metodológicos que estão na base de constituição histórica da cultura profissional renovada, expressos na direção social estratégica da profissão de Serviço Social e sua diretriz, o Projeto Ético-Político profissional. Produto de estudos pós-doutorais, e de duas pesquisas em andamento desde 2019, neste manuscrito realizamos uma discussão em torno do caldo sócio-histórico que fermentou na sociedade brasileira, no início da década de 1980, enfatizando o conteúdo tático-estratégico formulado pela classe trabalhadora brasileira, a chamada “estratégia democrático-popular” e suas incidências no Serviço Social. Nesta direção, visa contribuir com novas mediações para o entendimento dessa relação nos fundamentos do Projeto Ético-Político, considerando a ausência de análises a partir deste enfoque. Palavras-Chave: estratégia democrático-popular; cultura profissional renovada; projeto ético-político; direção social estratégica.
Promoção da adequada nutrição materna no serviço público-privado: a importância da suplementação
Authors: Machado Priscila Coelho Rabelo , Smiderle Fabiana Rosa Neves 
Published: September 2023

A assistência gestacional ocorre nos âmbitos público e privado. Nesse cuidado, destaca-se a maior demanda nutricional na gestação, à mãe e ao feto. Das causas de mortalidade infantil, destacam-se: baixo peso ao nascer; prematuridade e pré-natal inadequado. No cenário social de baixa renda, a nutrição é falha. Assim o suplemento alimentar tem extrema importância no cuidado pré-natal. Objetiva-se descrever a suplementação alimentar mais adequada à gestante, seja no setor público ou privado, destacando a política nacional, após revisão bibliográfica, realizada de maio a agosto de 2022. No Brasil mais de 70% das gestantes têm ganho de peso, porém com padrão nutricional pobre. Na atenção pré-natal pública no Brasil, são ofertados ácido fólico e ferro. A suplementação materna polivitamínica, com outros nutrientes além do ferro e folato, como vitaminas D, A, E, C, zinco, magnésio e outros, é importante. A problemática nutricional materna pública engloba fatores socioeconômicos, bem como falhas na assistência. A divergência com a atenção privada, prevalente em países desenvolvidos, é notória ao observar a mortalidade materna. Nos países periféricos a morte materna é 50 a 100 vezes maior que nos centrais. Nesses, mais de 90% das gestantes recebem suplementação polivitamínica. Palavras-Chave: nutrição materna; saúde materno-infantil; suplementos nutricionais; política de saúde; cuidado pré-natal.
Experiences of Portuguese Women in the Precariat: Between Frustration and the Lack of Meaning in the Future
Authors: Ornelas Marta Gorete Rodrigues , Matos Fátima Regina Ney , De Mesquita Rafael Fernandes 
Published: September 2023

How does the growing precariousness in employment and labor relations impact the construction of subjectivities and the personal and professional narratives of Portuguese working women? This research focuses on one of the distinctive aspects of this “class” – the precariat, which refers to highly educated young adults with jobs below these qualifications –, with the relations of production. More specifically, it focuses on women who believed that higher education would allow them to have a safe career/work trajectory. We conducted interviews with highly educated young women and adult women with precarious jobs, who perform functions below their academic qualifications. The collected data were analyzed using qualitative content analysis techniques, with the aid of the software Atlas/TI. The results show how precariousness means not only the uncertainty of salaried work but also, and above all, uncertainty as a way of life, of forms of subjection, and of bodies. This uncertainty extends to the whole sphere of life, producing subjectivities marked by anxiety, stress, pain, vulnerability, frustration, and hopelessness concerning the future. Keywords: precariat; precariousness; women; governmentality; subjectivities. Resumo — Como a crescente precariedade no emprego e nas relações de trabalho tem impacto na construção de subjetividades e nas narrativas pessoais e profissionais das mulheres portuguesas trabalhadoras? A investigação centra-se num dos aspectos distintivos desta “classe” - o precariado, que se refere aos jovens adultos com alta qualificação e trabalhos aquém desta -, com as relações de produção, especificamente no caso das mulheres que acreditavam que o ensino superior lhes permitiria ter uma carreira/trajetória segura de trabalho. Realizamos entrevistas com mulheres altamente qualificadas que estão em trabalhos precários, em que desempenham funções abaixo de suas qualificações acadêmicas. Os dados coletados foram analisados com técnicas de análise de conteúdo qualitativa, com auxílio do software Atlas/TI. Os resultados mostram como a precariedade não significa apenas a incerteza do trabalho assalariado, mas também e, sobretudo, a incerteza como modo de viver, dos modos de subjetivação e dos corpos. Incerteza que se estende à toda a esfera da vida, produzindo subjetividades marcadas por ansiedade, estresse, dor, vulnerabilidade, frustração e desesperança em relação ao futuro. Palavras-chave: precariado; precariedade; mulheres; governamentalidade; subjetividades.