Miracle-dz/UniFAR-FTUs huggingface dataset:
Shear Strength Properties of Coarse-Grained Soils Determined Using Large-Size Direct Shear Test

Abstract The paper deals with an analysis of the shear strength behaviour of coarse-grained materials using large-sized direct shear apparatus. The shear strength curve of compacted coarse-grained material allows for determining the three typical shear strengths, i.e. the shear strength for a maximum density of the sample tested (shear strength at point A), the peak shear strength (shear strength at point P), and the critical shear strength achieved for a large horizontal movement (shear strength at point C). Professional laboratories usually apply for determining the critical shear strength two different methods. The first method considers the critical shear strength at point A and the second method considers the critical shear strength at point C. The aim of the article is not to critically evaluate both methods, but to analyze the results of shear tests of gravels. The results of a large series of tests showed that these stresses may differ from each other in some cases, especially for poorly graded materials. In the case of sandy soil, the shear strength at point A and at point C is equal. However, in the case of poorly graded gravel, the shear strength at point C is greater than the shear strength at point A. The greatest difference between these shear strengths was measured in the case of poorly graded medium gravels. The results showed that the ratio of shear strength at point C to the shear strength at point A increases with increasing the grain size of the material tested. The peak as well as the critical shear strength parameters of poorly graded gravels is better represented by a multi-linear or a nonlinear failure line.
Finite Element and Artificial Neural Network Modeling of FRP-RC Columns Under Axial Compression Loading

The use of fiber-reinforced polymer (FRP) bars to overcome the corrosion problems in various reinforced concrete structures is now well documented in the literature. As a result, the currently available design guidelines such as North American design codes allow for using the FRP bars as alternative materials to steel bars to be incorporated into the concrete structures. In practice, hollow-core concrete columns (HCCs) are widely accepted to make a lightweight structure and reduce its cost. Due to the lack of laboratory tests, engineers may not perform a safe design of HCCs with internal FRP bars. Therefore, the presented paper has endeavored to numerically and theoretically explore using the FRP bars and spirals as internal reinforcement for HCCs and investigate the effects of several test parameters. Using the current version of Finite Element Analysis (FEA) ABAQUS (3DS, 2014), a total of 116 HCCs were simulated based on 29 specimens experimentally tested by the researchers which acted as control specimens for the FE model. The complex structural response of concrete was reasonably determined using the concrete damaged plasticity model (CDPM) and the mechanical response of the FRP rebars are considered to behave linearly up to failure with no yielding stage. The calibrated FE model can provide an excellent portrayal of the HCCs’ response. Based on the database obtained from laboratory and simulation, several Artificial Neural Network (ANN) models were further provided to predict the confined compressive load of GFRP-RC HCCs at different loading stages.
Lung Cancer Treatment: From Tradition to Innovation

Lung cancer (LC) is the second most commonly diagnosed cancer and the primary cause of cancer death worldwide in 2020. LC treatment is associated with huge costs for patients and society; consequently, there is an increasing interest in the prevention, early detection with screening, and development of new treatments. Its surgical management accounts for at least 90% of the activity of thoracic surgery departments. Surgery is the treatment of choice for early-stage non-small cell LC. In this article, we discuss the state of the art of thoracic surgery for surgical management of LC. We start by describing the milestones of LC treatment, which are lobectomy and an adequate lymphadenectomy, and then we focus on the traditional and innovative minimally invasive surgical approaches available: video-assisted thoracoscopic surgery (VATS) and robotic-assisted thoracoscopic surgery (RATS). A brief overview of the innovation and future perspective in thoracic surgery will close this mini-review.
The Antibiofilm Role of Biotics Family in Vaginal Fungal Infections

“Unity in strength” is a notion that can be exploited to characterize biofilms as they bestow microbes with protection to live freely, escalate their virulence, confer high resistance to therapeutic agents, and provide active grounds for the production of biofilms after dispersal. Naturally, fungal biofilms are inherently resistant to many conventional antifungals, possibly owing to virulence factors as their ammunitions that persistently express amid planktonic transition to matured biofilm state. These ammunitions include the ability to form polymicrobial biofilms, emergence of persister cells post-antifungal treatment and acquisition of resistance genes. One of the major disorders affecting vaginal health is vulvovaginal candidiasis (VVC) and its reoccurrence is termed recurrent VVC (RVVC). It is caused by the Candida species which include Candida albicans and Candida glabrata. The aforementioned Candida species, notably C. albicans is a biofilm producing pathogen and habitually forms part of the vaginal microbiota of healthy women. Latest research has implicated the role of fungal biofilms in VVC, particularly in the setting of treatment failure and RVVC. Consequently, a plethora of studies have advocated the utilization of probiotics in addressing these infections. Specifically, the excreted or released compounds of probiotics which are also known as postbiotics are being actively researched with vast potential to be used as therapeutic options for the treatment and prevention of VVC and RVVC. These potential sources of postbiotics are harnessed due to their proven antifungal and antibiofilm. Hence, this review discusses the role of Candida biofilm formation in VVC and RVVC. In addition, we discuss the application of pro-, pre-, post-, and synbiotics either individually or in combined regimen to counteract the abovementioned problems. A clear understanding of the role of biofilms in VVC and RVVC will provide proper footing for further research in devising novel remedies for prevention and treatment of vaginal fungal infections.
A Comprehensive Database for DNA Adductomics

The exposure of human DNA to genotoxic compounds induces the formation of covalent DNA adducts, which may contribute to the initiation of carcinogenesis. Liquid chromatography (LC) coupled with high-resolution mass spectrometry (HRMS) is a powerful tool for DNA adductomics, a new research field aiming at screening known and unknown DNA adducts in biological samples. The lack of databases and bioinformatics tool in this field limits the applicability of DNA adductomics. Establishing a comprehensive database will make the identification process faster and more efficient and will provide new insight into the occurrence of DNA modification from a wide range of genotoxicants. In this paper, we present a four-step approach used to compile and curate a database for the annotation of DNA adducts in biological samples. The first step included a literature search, selecting only DNA adducts that were unequivocally identified by either comparison with reference standards or with nuclear magnetic resonance (NMR), and tentatively identified by tandem HRMS/MS. The second step consisted in harmonizing structures, molecular formulas, and names, for building a systematic database of 279 DNA adducts. The source, the study design and the technique used for DNA adduct identification were reported. The third step consisted in implementing the database with 303 new potential DNA adducts coming from different combinations of genotoxicants with nucleobases, and reporting monoisotopic masses, chemical formulas, . cdxml files, . mol files, SMILES, InChI, InChIKey and IUPAC nomenclature. In the fourth step, a preliminary spectral library was built by acquiring experimental MS/MS spectra of 15 reference standards, generating in silico MS/MS fragments for all the adducts, and reporting both experimental and predicted fragments into interactive web datatables. The database, including 582 entries, is publicly available (https://gitlab.com/nexs-metabolomics/projects/dna_adductomics_database). This database is a powerful tool for the annotation of DNA adducts measured in (HR)MS. The inclusion of metadata indicating the source of DNA adducts, the study design and technique used, allows for prioritization of the DNA adducts of interests and/or to enhance the annotation confidence. DNA adducts identification can be further improved by integrating the present database with the generation of authentic MS/MS spectra, and with user-friendly bioinformatics tools.
Bottom-Up Control of the Groundwater Microbial Food-Web in an Alpine Aquifer

Groundwater ecosystems are typically poor in organic carbon and productivity sustaining a low standing stock of microbial biomass. In consequence, microbial food webs in oligotrophic groundwater are hypothesized to be bottom-up controlled. To date, quantitative information on groundwater microbial communities, food web interactions, and carbon flow is relatively lacking in comparison to that of surface waters. Studying a shallow, porous alpine aquifer we collected data on the numbers of prokaryotes, virus-like particles and heterotrophic nanoflagellates (HNFs), the concentration of dissolved (DOC) and assimilable organic carbon (AOC), bacterial carbon production (BCP), and physical-chemical conditions for a 1 year hydrological cycle. The potential effects of protozoan grazing and viral lysis onto the prokaryotic biomass was tested. Flow of organic carbon through the microbial food web was estimated based on data from the literature. The abundance of prokaryotes in groundwater was low with 6.1 ± 6.9 × 104 cells mL–1, seasonally influenced by the hydrological dynamics, with higher densities coinciding with a lower groundwater table. Overall, the variability in cell numbers was moderate, and so it was for HNFs (179 ± 103 HNFs mL–1) and virus-like particles (9.6 ± 5.7 × 105 VLPs mL–1). The virus to prokaryotes and prokaryote to HNF ratios ranged between 2–230 and 33–2,084, respectively. We found no evidence for a viral control of prokaryotic biomass, and the biomass of HNFs being bottom-up controlled. First estimations point at carbon use efficiencies of 0.2–4.2% with prokaryotic production, and carbon consumed and recycled by HNFs and phages to be of minor importance. This first groundwater microbial food web analysis strongly hints at a bottom-up control on productivity and standing stock in oligotrophic groundwater ecosystems. However, direct measurement of protozoan grazing and phage mediated lysis rates of prokaryotic cells are urgently needed to deepen our mechanistic understanding. The effect of microbial diversity on the population dynamics still needs to be addressed.
The Investigation of Hepatitis B Vaccine Immune Responses in Occult Hepatitis B Virus-Infected Patients

Objectives There is no effective treatment for occult hepatitis B virus infection (OBI) patients, and immunotherapy may be one of the most promising options. We aim to investigate the underlying mechanism and therapeutic potential of hepatitis B vaccine immunotherapy for OBI patients. Methods Outpatient OBI patients were screened and randomly divided into treatment (Group A) and control (Group B) groups. At weeks 0, 4, and 24, patients in Group A received a subcutaneous/intramuscular injection of hepatitis B vaccine (Engerix-B, 20 μg/time) according to the standard vaccination schedule; patients in Group B served as blank control. The patients were followed for 36 weeks, with clinical, biochemical, virological, immunological, and imaging data collected and analyzed at weeks 0, 12, 24, and 36, respectively, and the relation between the virology and immunology results was analyzed. Results Of the 228 OBI patients, 28 were excluded, and 200 were enrolled for observation. In the end, 44 patients were included in Group A and 39 in Group B after excluding lost cases. At week 0 (baseline), some patients in two groups had liver disease symptoms, HBV-related liver function damage, and liver fibrosis. 86.36% (38/44) and 82.05% (32/39) patients were positive for serum hepatitis B surface antibodies (anti-HBs) in Group A and Group B, respectively, with the median (quartile) of 42.47 (16.85, 109.1) and 39.27 (16.06, 117.4) mIU/ml, respectively. Reduced peripheral blood CD4+T, CD8+T, and B lymphocytes were found in some patients in two groups. These results were not statistically different between Group A and Group B (P>0.05). At week 36, all patients were serum anti-HBs (+) in Group A, with a median (quartile) of 1000 (483.9, 1000) mIU/ml, which was significantly higher than that at week 0 (P<0.05) and that in Group B (P<0.05). Compared to week 0, the number of CD8+ T and B lymphocytes increased significantly and were significantly higher than Group B at the same point. Two patients in Group B were found to have hepatitis B virus reactivation from week 12 to week 36. Correlation Analysis Anti-HBs in Group A patients were positively correlated with B lymphocytes (r=0.3431, 0.3087, and 0.3041, respectively) and positively correlated with CD8+ T lymphocytes (r=0.4954, 0.3054, and 0.3455, respectively) at weeks 12, 24, and 36. Conclusion Virological reactivation is a risk for OBI patients. Serum hepatitis B surface antibodies were significantly increased after hepatitis B vaccine treatment, the same as the numbers of peripheral blood B and CD8+ T lymphocytes; changes in hepatitis B surface antibody levels were positively correlated with the changes in peripheral blood B and CD8+ T lymphocytes.
Evaluation of Patients With Cognitive Impairment Due to Suspected Idiopathic Normal-Pressure Hydrocephalus at Medical Centers for Dementia: A Nationwide Hospital-Based Survey in Japan

Objective Treatment of idiopathic normal-pressure hydrocephalus (iNPH) requires collaboration between dementia specialists and neurosurgeons. The role of dementia specialists is to differentiate patients with iNPH from patients with other dementia diseases and to determine if other dementia diseases are comorbid with iNPH. We conducted a nationwide hospital-based questionnaire survey on iNPH in medical centers for dementia (MCDs). Methods We developed a questionnaire to assess how physicians in MCDs evaluate and treat patients with cognitive impairment due to suspected iNPH and the difficulties these physicians experience in the evaluation and treatment of patients. The questionnaire was sent to all 456 MCDs in Japan. Results Questionnaires from 279 MCDs were returned to us (response rate: 61.2%). Patients underwent cognitive tests, evaluation of the triad symptoms of iNPH, and morphological neuroimaging examinations in 96.8, 77.8, and 98.2% of the MCDs, respectively. Patients with suspected iNPH were referred to other hospitals (e.g., hospitals with neurosurgery departments) from 78.9% of MCDs, and cerebrospinal fluid (CSF) tap test was performed in 44 MCDs (15.8%). iNPH guidelines (iNPHGLs) and disproportionately enlarged subarachnoid space hydrocephalus (DESH), a specific morphological finding, were used and known in 39.4% and 38% of MCDs, respectively. Logistic regression analysis with “Refer the patient to other hospitals (e.g., hospitals with neurosurgery departments) when iNPH is suspected. ” as the response variable and (a) using the iNPHGLs, (b) knowledge of DESH, (c) confidence regarding DESH, (d) difficulty with performing brain magnetic resonance imaging, (e) knowledge of the methods of CSF tap test, (f) absence of physician who can perform lumbar puncture, and (g) experience of being told by neurosurgeons that referred patients are not indicated for shunt surgery as explanatory variables revealed that the last two factors were significant predictors of patient referral from MCDs to other hospitals. Conclusion Sufficient differential or comorbid diagnosis using CSF tap test was performed in a few MCDs. Medical care for patients with iNPH in MCDs may be improved by having dementia specialists perform CSF tap tests and share the eligibility criteria for shunt surgery with neurosurgeons.
The Olfactory Organ Is a Unique Site for Neutrophils in the Brain

In the vertebrate olfactory tract new neurons are continuously produced throughout life. It is widely believed that neurogenesis contributes to learning and memory and can be regulated by immune signaling molecules. Proteins originally identified in the immune system have subsequently been localized to the developing and adult nervous system. Previously, we have shown that olfactory imprinting, a specific type of long-term memory, is correlated with a transcriptional response in the olfactory organs that include up-regulation of genes associated with the immune system. To better understand the immune architecture of the olfactory organs we made use of cell-specific fluorescent reporter lines in dissected, intact adult brains of zebrafish to examine the association of the olfactory sensory neurons with neutrophils and blood-lymphatic vasculature. Surprisingly, the olfactory organs contained the only neutrophil populations observed in the brain; these neutrophils were localized in the neural epithelia and were associated with the extensive blood vasculature of the olfactory organs. Damage to the olfactory epithelia resulted in a rapid increase of neutrophils both within the olfactory organs as well as the central nervous system. Analysis of cell division during and after damage showed an increase in BrdU labeling in the neural epithelia and a subset of the neutrophils. Our results reveal a unique population of neutrophils in the olfactory organs that are associated with both the olfactory epithelia and the lymphatic vasculature suggesting a dual olfactory-immune function for this unique sensory system.
Dietary Acid Load Is Positively Associated With Risk of Gestational Diabetes Mellitus in a Prospective Cohort of Chinese Pregnant Women

Background Growing evidence suggests that dietary acid load plays an important role in the development of type 2 diabetes. However, prospective studies on the relationship between dietary acid load and gestational diabetes mellitus (GDM) are limited in the pregnant population. This study aimed to investigate the effect of dietary acid load during early pregnancy on the risk of GDM in Chinese pregnant women. Methods A total of 1,327 pregnant women were enrolled from an ongoing prospective study of the Tongji Birth cohort (TJBC) in Wuhan, China. Dietary intake was assessed before 20 weeks using a 74-item semiquantitative food frequency questionnaire (FFQ). The dietary acid load was estimated using potential renal acid load (PRAL), net endogenous acid production (NEAP), and animal protein to potassium ratio (A:P ratio). A 75g 2-h oral glucose tolerance test (OGTT) was performed at 24-28 gestational weeks to diagnose GDM. Results The mean (standard deviation) values for PRAL score, NEAP score, and A:P ratio were 0.8 ± 11.3 mEq/day, 45.3 ± 16.5 mEq/day, and 9.8 ± 6.0, respectively. There was a significant positive correlation of dietary acid load with the intake of red meat, poultry, fish, and eggs, and a negative correlation with the intake of vegetables, fruits, nuts, and legumes (all P < 0.05). Compared to the lowest tertile, the highest tertile of dietary acid load, including PRAL score (odds ratio [OR]: 2.26, 95% confidence interval [CI] = 1.38–3.71, P-trend = 0.002), NEAP score (OR: 2.02, 95% CI = 1.25–3.27, P-trend = 0.009), and A:P ratio (2.08, 95% CI = 1.30–3.31, P-trend = 0.005), significantly increased the risk of GDM. In addition, the dietary acid load was also significantly associated with an increase in 1-h and 2-h post-load blood glucose concentrations (all P-trend < 0.05). Conclusion We found a significant positive association between dietary acid load during early pregnancy and the risk of GDM in a Chinese population, suggesting that the reduction of food sources of dietary acid load may be an effective strategy for preventing the risk of GDM.
Football and Dementia: Understanding the Link

Football, also known as soccer or association football, is popular but has a potential link with dementia developing in retired players. The FA and soccer regulators in the USA have imposed guidelines limiting players exposure to heading, despite controversy whether this dementia is caused by heading the ball, a form of mild repetitive head injury (RHI), over many years. Substantial data exist showing that many ex-North American Football players develop a specific neurodegenerative disease: chronic traumatic encephalopathy (CTE), the neuropathological disorder of boxers. In the United Kingdom evidence for the neuropathological basis of footballers' dementia has been slow to emerge. A 2017 study revealed that in six ex-soccer players four had CTE with Alzheimer's disease (AD) and two had AD. A 2019 study showed that ex-footballers were 3.5 times more likely to die from dementia or other neuro-degenerative diseases than matched controls. We argue that in childhood and adolescence the brain is vulnerable to heading, predicated on its disproportionate size and developmental immaturity. RHI in young individuals is associated with early neuroinflammation, a potential trigger for promoting neurodegeneration in later life. Evidence is available to support the guidelines limiting heading for players of all ages, while professional and non-players should be included in prospective studies to investigate the link between soccer and dementia.
Sporotrichosis Caused by Non-Wild Type Sporothrix brasiliensis Strains

The zoonotic transmission of sporotrichosis due to Sporothrix brasiliensis occurs largely in Rio de Janeiro state, Brazil since the 1990´s. Most patients infected with S. brasiliensis respond well to itraconazole or terbinafine. However, a few patients have a slow response or do not respond to the treatment and develop a chronic infection. The aim of this study was to analyze strains of S. brasiliensis against five different drugs to determine minimal inhibitory concentration distributions, to identify non-wild type strains to any drug evaluated and the clinical aspects of infections caused by them. This study evaluated 100 Sporothrix spp. strains obtained from 1999 to 2018 from the Evandro Chagas National Institute of Infectious Diseases, Fiocruz, which were identified through a polymerase chain reaction using specific primers for species identification. Two-fold serial dilutions of stock solutions of amphotericin B, itraconazole, posaconazole, ketoconazole and terbinafine prepared in dimethyl sulfoxide were performed to obtain working concentrations of antifungal drugs ranging from 0.015 to 8.0 mg/L. The broth microdilution reference method was performed according the M38-A2 CLSI guideline. All strains were identified as S. brasiliensis and thirteen were classified as non-wild type, two of them against different drugs. Non-wild type strains were identified throughout the entire study period. Patients infected by non-wild type strains presented prolonged treatment times, needed increased antifungal doses than those described in the literature and one of them presented a permanent sequel. In addition, three of them, with immunosuppression, died from sporotrichosis. Despite the broad use of antifungal drugs in hyperendemic areas of sporotrichosis, an emergence of non-wild type strains did not occur. The results of in vitro antifungal susceptibility tests should guide sporotrichosis therapy, especially in immunosuppressed patients.