Miracle-dz/UniFAR-FTUs huggingface dataset:
The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial

Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum, and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ); the most (relative) abundant being uncharacterized species within the genera Methylobacillus, Solirubrobacter, and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis, Methylophilus methylotrophus, Nitrosospira, and Lysobacter mobilis. The capacity to track alterations of an amplified microbial community at high taxonomic resolution using modern bioinformatic approaches, as well as identifying where that resolution is lost for technical or biological reasons, provides an insight into the complexity of the microbial world resisting anthropogenic pollution. While functional assessment of uncharacterized organisms within environmental samples is technically challenging, an important step is observing those organisms able to tolerate extreme stress and to recognize the extent to which important amplifiable community members still require characterization.
Identification of “BRAF-Positive” Cases Based on Whole-Slide Image Analysis

A key requirement for precision medicine is the accurate identification of patients that would respond to a specific treatment or those that represent a high-risk group, and a plethora of molecular biomarkers have been proposed for this purpose during the last decade. Their application in clinical settings, however, is not always straightforward due to relatively high costs of some tests, limited availability of the biological material and time, and procedural constraints. Hence, there is an increasing interest in constructing tissue-based surrogate biomarkers that could be applied with minimal overhead directly to histopathology images and which could be used for guiding the selection of eventual further molecular tests. In the context of colorectal cancer, we present a method for constructing a surrogate biomarker that is able to predict with high accuracy whether a sample belongs to the “BRAF-positive” group, a high-risk group comprising V600E BRAF mutants and BRAF-mutant-like tumors. Our model is trained to mimic the predictions of a 64-gene signature, the current definition of BRAF-positive group, thus effectively identifying histopathology image features that can be linked to a molecular score. Since the only required input is the routine histopathology image, the model can easily be integrated in the diagnostic workflow.
Clinical significance and diagnostic capacity of serum TK1, CEA, CA 19-9 and CA 72-4 levels in gastric and colorectal cancer patients

Despite extensive progress in treatment for cancer in recent decades, the early diagnosis for gastric cancer (GC) and colorectal cancer (CRC) remains poor. In this study, we explore the diagnostic value of joint detection of thymidine kinase 1 (TK1), carcinoembryonic antigen (CEA), carbohydrate antigen 19-9 (CA 19-9) and carbohydrate antigen 72-4 (CA 72-4) in the diagnosis of GC and CRC, and to evaluated the relationship between TK1 expression and clinical pathological characteristics in the patients. Serum TK1, CA 19-9, CA 72-4 and CEA levels were measured in 169 patients with GC, 344 patients with CRC and 75 healthy controls using electro-chemiluminescence. The TK1 concentration was significantly higher in patients with cancer than in healthy controls and patients with clinical stage Ⅲ+Ⅳ had higher TK1 levels than clinical stage Ⅰ+Ⅱ (P<0.05). The levels of TK1 is significantly associated with tumor stage, lymph node metastasis, distant metastasis, tumor differentiation and age (P<0.05). When the tumor markers (TK1, CA 19-9 and CA 72-4) were detected respectively, the area under receiver operating characteristics curve (AUC) of TK1 for three cancers was the highest (0.823-0.895). However, the combination of AUC was higher than that for each tumor marker detected respectively (0.934-0.953), and the Hosmer-Lemeshow test showed an adequate model of calibration (P>0.05). Moreover, the AUCs varied significantly between the combination tests and single biomarker tests (Z test, P<0.01). In conclusion, serum TK1 may be an independent tumor marker for GC and CRC patients, and the combination of TK1, CA 19-9 and CA 72-4 and CEA performed even better. This study suggests that combination detection of four tumor markers may prove to be useful for the diagnosis of GC and CRC.
Microleakage of newly developed nano-ionomer and glass ionomer cement restoration

Objectives: The aim of this in-vitro study was to evaluate the marginal integrity and microleakage of newly developed nano-ionomer and glass ionomer cement after thermocycling and heating. Methods: The materials tested were nano-ionomer (Glass Carbomer, Glass Carbomer® Products, LOT 8803839) and fast setting glass ionomer (GC Fuji IX GP EXTRA, GC, LOT 0801163). Ten specimens were assigned to each material, restored and cured using an external heat source (Bluephase 16i, Ivoclar Vivadent) for 40s according manufacturer's instructions. Class V restorations were placed on lingually and vestibulary surface of each tooth filled with tested materials. All samples were stored in distilled water at 37°C for 24 hours and then thermocycled in 5°C and 55°C water bath for 1800 cycles with a 10s dwell time. After thermocycling the teeth were immersed in a silver nitrate dye solution for 24 h and embedded in acrylic resin. Samples were sectioned longitudinally through the center of the restoration. The sections were examined for microleakage. The microleakage scores were determined using the dye penetration distance ratio according to Oberholzer. The worst score of microleakage per restoration were calculated. Data were statistically analyzed by using Kruskal-Wallis and Mann-Whitney U-test. Results: The heat-cured Glass Carbomer showed lower microleakage values than fast setting glass ionomer although there were no statistically significant differences between tested materials. Conclusion: This in-vitro study emphasized the efficacy of nano-ionomer cements that can be used in routine clinical practice.
Characterization of Renal Injury and Inflammation in an Experimental Model of Intravascular Hemolysis

Intravascular erythrocyte destruction, accompanied by the release of pro-oxidative and pro-inflammatory components hemoglobin and heme, is a common event in the pathogenesis of numerous diseases with heterogeneous etiology and clinical features. A frequent adverse effect related to massive hemolysis is the renal injury and inflammation. Nevertheless, it is still unclear whether heme––a danger-associated molecular pattern––and ligand for TLR4 or upstream hemolysis-derived products are responsible for these effects. Well-characterized animal models of hemolysis with kidney impairment are needed to investigate how hemolysis drives kidney injury and to test novel therapeutic strategies. Here, we characterized the pathological processes leading to acute kidney injury and inflammation during massive intravascular hemolysis, using a mouse model of phenylhydrazine (PHZ)-triggered erythrocyte destruction. We observed profound changes in mRNA levels for markers of tubular damage (Kim-1, NGAL) and regeneration (indirect marker of tubular injury, Ki-67), and tissue and vascular inflammation (IL-6, E-selectin, P-selectin, ICAM-1) in kidneys of PHZ-treated mice, associated with ultrastructural signs of tubular injury. Moreover, mass spectrometry revealed presence of markers of tubular damage in urine, including meprin-α, cytoskeletal keratins, α-1-antitrypsin, and α-1-microglobulin. Signs of renal injury and inflammation rapidly resolved and the renal function was preserved, despite major changes in metabolic parameters of PHZ-injected animals. Mechanistically, renal alterations were largely heme-independent, since injection of free heme could not reproduce them, and scavenging heme with hemopexin in PHZ-administered mice could not prevent them. Reduced overall health status of the mice suggested multiorgan involvement. We detected amylasemia and amylasuria, two markers of acute pancreatitis. We also provide detailed characterization of renal manifestations associated with acute intravascular hemolysis, which may be mediated by hemolysis-derived products upstream of heme release. This analysis provides a platform for further investigations of hemolytic diseases and associated renal injury and the evaluation of novel therapeutic strategies that target intravascular hemolysis.
A new comprehensive model for Continuous Professional Development

Abstract Background: It is generally agreed that continuing professional development (CPD) for GPs is important for quality of care. Internationally, however, different approaches to identify the learning objectives and the CPD content have been chosen. Objectives: To improve GPs’ CPD in Denmark we explore how general practitioners’ (GPs) self-experienced learning needs can be combined with learning needs experienced from a societal perspective and still make sense for GPs. Methods: We performed a multi-dimensional learning needs analysis with a modified Delphi method in a participatory action research set-up. Twenty practice-based small learning groups and a group appointed by the Danish public health service were asked to identify learning needs with the Danish family medicine curriculum as reference. Then we asked a group of GP researchers and hospital consultants, a group of GPs with interests in narrative, person-centred medicine and a group of GP educators, and administrative staff, to triangulate the initial findings. Results: We identified educational themes through a defined collaborative consensus oriented process. Examples of themes are the diagnostic challenge, care for patients with multi-morbidity, elderly patients and children. Due to variation in requested learning objectives, the identified themes do not cover all relevant areas for CPD training. The identified themes will only make sense if seen as supplementary to other CPD activities based on GPs individual needs analyses. Conclusion: It is possible to identify prioritized educational themes for GPs through a process involving the majority of stakeholders. Nevertheless, CPD should also include activities based on individual needs analysis. KEY MESSAGES When developing a continuing professional development programme for GPs, educational themes can be identified by a multi-dimensional needs analysis involving different stakeholders. GPs might benefit from activities based on a consensus-based curriculum combined with an individual needs analysis, thus exposing individual GPs to both recognized and non-recognized relevant learning needs.
The measurement of cognitive reactivity to sad mood in patients remitted from major depressive disorder

Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva. nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible.
coxphMIC: An R Package for Sparse Estimation of Cox Proportional Hazards Models via Approximated Information Criteria

In this paper, we describe an R package named coxphMIC, which implements the sparse estimation method for Cox proportional hazards models via approximated information criterion (Su et al., 2016 Biometrics). The developed methodology is named MIC which stands for "Minimizing approximated Information Criteria". A reparameterization step is introduced to enforce sparsity while at the same time keeping the objective function smooth. As a result, MIC is computationally fast with a superior performance in sparse estimation. Furthermore, the reparameterization tactic yields an additional advantage in terms of circumventing post-selection inference. The MIC method and its R implementation are introduced and illustrated with the PBC data.
Effects of diphyllin as a novel V-ATPase inhibitor on TE-1 and ECA-109 cells

Diphyllin is a natural component of traditional Chinese medicine, which effectively inhibits V-ATPase activity and affects the progression of cancer. However, few studies have been conducted on esophageal cancer, and the mechanisms remain to be elucidated. The present study revealedthat diphyllin inhibited proliferation and induced S arrest in esophageal cancer cell lines TE-1 and ECA-109. Further experiments revealed that diphyllin inhibited V-ATPase activity and decreased the mRNA expression of mammalian target of rapamycin complex 1 (mTORC1), hypoxia-inducible factor-1α (HIF-1α), and vascular endothelial growth factor (VEGF). The present study also revealed that diphyllin inhibited proliferation and reduced the formation of new blood vessels. Diphyllin inhibited blood metastasis by regulating the mTORC1/HIF-1α-/VEGF pathway, therefore it could be considered as a new V-ATPase inhibitor to treat esophageal cancer.
Systemic Arterial Hypertension in Patients Exposed to Cesium-137 in Goiânia-GO: Prevalence Study

Background: Systemic Arterial Hypertension (SAH) in the Brazilian population, in populations not exposed to Césio-137, presents a prevalence of 28% nationwide. However, in the group of radioactivity victims, these values are unknown. Objective: To analyze the prevalence of hypertension in patients exposed to Cesium-137 in Goiânia, enrolled in the Sistema de Monitoramento dos Radioacidentados (SISRAD) (Radioactivtity Victims Monitoring System) of the Centro de Assistência aos Radioacidentados (C.A.R.A) (Assistence Center for Radioactivity Victims). Methods: This is a descriptive, observational cross-sectional epidemiological study carried out in Goiânia-Goiás, from August 2013 to October 2014, with a group of patients enrolled in the Sistema de Monitoramento dos Radioacidentados (SISRAD) of the Centro de Assistência a Radioacidentados (C.A.R.A.). A total of 102 radioactive patients were divided into two groups: group 1 with 40 and group 2 with 62 participants. A field survey was conducted with a closed and semi-structured questionnaire in which the following contexts were addressed: sociodemographic profile, life habits and personal background. A database was created using the Google Forms application from the Google Web technologies company. The duly collected and stored data were imported and analyzed in the statistical software SPSS, version 21. Results: The prevalence of SAH reached a total of 25% (12 individuals) of the 48 interviewees, 50% of women (24) and 50% of men (24), of which 22.9% (11) of the radioactivity victims revealed to be smokers. Conclusion: The prevalence of SAH in the radioactivity victims population is similar to that of the population in general.
Incidence, etiology, and outcome of bacterial meningitis in infants aged <90 days in the United kingdom and Republic of Ireland: prospective, enhanced, national population-based surveillance.

BACKGROUND Bacterial meningitis remains a major cause of morbidity and mortality in young infants. Understanding the epidemiology and burden of disease is important. METHODS Prospective, enhanced, national population-based active surveillance was undertaken to determine the incidence, etiology, and outcome of bacterial meningitis in infants aged <90 days in the United Kingdom and Ireland. RESULTS During July 2010-July 2011, 364 cases were identified (annual incidence, 0.38/1000 live births; 95% confidence interval [CI], .35-.42). In England and Wales, the incidence of confirmed neonatal bacterial meningitis was 0.21 (n = 167; 95% CI, .18-.25). A total of 302 bacteria were isolated in 298 (82%) of the cases. The pathogens responsible varied by route of admission, gestation at birth, and age at infection. Group B Streptococcus (GBS) (150/302 [50%]; incidence, 0.16/1000 live births; 95% CI, .13-.18) and Escherichia coli (41/302 [14%]; incidence, 0.04/1000; 95% CI, .03-.06) were responsible for approximately two-thirds of identified bacteria. Pneumococcal (28/302 [9%]) and meningococcal (23/302 [8%]) meningitis were rare in the first month, whereas Listeria meningitis was seen only in the first month of life (11/302 [4%]). In hospitalized preterm infants, the etiology of both early- and late-onset meningitis was more varied. Overall case fatality was 8% (25/329) and was higher for pneumococcal meningitis (5/26 [19%]) than GBS meningitis (7/135 [5%]; P = .04) and for preterm (15/90 [17%]) compared with term (10/235 [4%]; P = .0002) infants. CONCLUSIONS The incidence of bacterial meningitis in young infants remains unchanged since the 1980s and is associated with significant case fatality. Prevention strategies and guidelines to improve the early management of cases should be prioritized.
Autologous Bone Marrow Concentrates and Concentrated Growth Factors Accelerate Bone Regeneration After Enucleation of Mandibular Pathologic Lesions

Abstract Stem cell therapy is a revolutionary new way to stimulate mesenchymal tissue regeneration. The platelets concentrate products started with platelet-rich plasma (PRP), followed by platelet-rich fibrin (PRF), whereas concentrated growth factors (CGF) are the latest generation of the platelets concentrate products which were found in 2011. The aim of the present study was to evaluate the potential of combining autologous bone marrow concentrates and CGF for treatment of bone defects resulting from enucleation of mandibular pathologic lesions. Twenty patients (13 males and 7 females) with mandibular benign unilateral lesions were included, and divided into 2 groups. Group I consisted of 10 patients who underwent enucleation of the lesions followed by grafting of the bony defects with autologous bone marrow concentrates and CGF. Group II consisted of 10 patients who underwent enucleation of the lesions without grafting (control). Radiographic examinations were done immediately postoperative, then at 1, 3, 6, and 12 months, to evaluate the reduction in size and changes in bone density at the bony defects. Results indicated a significant increase in bone density with respect to the baseline levels in both groups (P < 0.05). The increase in bone density was significantly higher in group I compared with group II at the 6- and 12-month follow-up examinations (P < 0.05). The percent of reduction in the defects’ size was significantly higher in group I compared with group II after 12 months (P = 0.00001). In conclusion, the clinical application of autologous bone marrow concentrates with CGF is a cost effective and safe biotechnology, which accelerates bone regeneration and improves the density of regenerated bone.
A Handheld and Textile-Enabled Bioimpedance System for Ubiquitous Body Composition Analysis. An Initial Functional Validation

In recent years, many efforts have been made to promote a healthcare paradigm shift from the traditional reactive hospital-centered healthcare approach towards a proactive, patient-oriented, and self-managed approach that could improve service quality and help reduce costs while contributing to sustainability. Managing and caring for patients with chronic diseases accounts over 75% of healthcare costs in developed countries. One of the most resource demanding diseases is chronic kidney disease (CKD), which often leads to a gradual and irreparable loss of renal function, with up to 12% of the population showing signs of different stages of this disease. Peritoneal dialysis and home haemodialysis are life-saving home-based renal replacement treatments that, compared to conventional in-center hemodialysis, provide similar long-term patient survival, less restrictions of life-style, such as a more flexible diet, and better flexibility in terms of treatment options and locations. Bioimpedance has been largely used clinically for decades in nutrition for assessing body fluid distributions. Moreover, bioimpedance methods are used to assess the overhydratation state of CKD patients, allowing clinicians to estimate the amount of fluid that should be removed by ultrafiltration. In this work, the initial validation of a handheld bioimpedance system for the assessment of body fluid status that could be used to assist the patient in home-based CKD treatments is presented. The body fluid monitoring system comprises a custom-made handheld tetrapolar bioimpedance spectrometer and a textile-based electrode garment for total body fluid assessment. The system performance was evaluated against the same measurements acquired using a commercial bioimpedance spectrometer for medical use on several voluntary subjects. The analysis of the measurement results and the comparison of the fluid estimations indicated that both devices are equivalent from a measurement performance perspective, allowing for its use on ubiquitous e-healthcare dialysis solutions.