Miracle-dz/UniFAR-FTUs huggingface dataset:
The challenges of image segmentation in big remotely sensed imagery data

With the increase in spatial, spectral and temporal resolutions of Earth observing systems, geospatial and remote sensing (RS) image research is shifting towards a big data paradigm. One of the most important challenges in RS big data is image segmentation, which is defined as a process to group pixels together by a predefined criteria. Image segmentation allows for the extraction of features such as roads or habitats or buildings. Image segmentation is rendered more difficult with big data because the computing power on single platforms cannot keep pace with the size and velocity of new data. Big data sets must be decomposed for the analysis in distributed and parallel computing platforms. Decomposition through techniques like slicing by spatial extent obscures the geometric and topological information in geospatial data, for example generating fake artefacts. To address these challenges, we propose a geospatial cyberinfrastructure (GCI) that coordinates cloud computing, MapReduce framework, image segmentation algorithms, a spatial extent splitting method and a recomposing technique using moving window. This GCI is evaluated on cloud computing to identify features in a 312.07 GB high-resolution colour aerial photo with Hadoop. K-means-based image segmentation is selected as the case study. We deploy the architecture in private cloud and public cloud implementation, respectively. The results demonstrate the benefits of the decomposing and recomposing methods in segmenting images, removing fake artefacts and reducing information distortion. More general problems in big data are revealed, among them I/O problems, particularly in the amount of preprocessing and post-processing that will be required in any analysis of big imagery data. We conclude with implications for scalability and suggestions to speed up decomposition and recomposition.
Current Clinical Evidence for Proton Therapy

Proton beam therapy provides the opportunity for more localized delivery of ionizing radiation with the potential for improved normal tissue avoidance to reduce treatment related morbidity and to allow for dose escalation to improve disease control and survival without increased toxicity. However, a systematic review of published peer-reviewed literature reported previously and updated here is devoid of any clinical data demonstrating benefit in terms of survival, tumor control, or toxicity in comparison with best conventional treatment for any of the tumors so far treated including skull base and ocular tumors, prostate cancer and childhood malignancies. The current lack of evidence for benefit of protons should provide a stimulus for continued research. Well designed in silico clinical trials using validated normal tissue complication probability-models are important to predict the magnitude of benefit for individual tumor sites but the future use of protons should be guided by clear evidence of benefit demonstrated in well-designed prospective studies, away from commercial influence, and this is likely to require international collaboration. Any complex and expensive technology, including proton therapy, should not be employed on the basis of belief alone and requires testing to avoid inappropriate use of potential detriment to future patients.
Estudo comparativo de três diferentes procedimentos para extração de RNA a partir de amostras fixadas em formalina e embebidas em parafina

INTRODUCAO: O desenvolvimento de metodos de extracao de RNA a partir de amostras fixadas em formalina e embebidas em parafina (FFEP) possibilitou estudos retrospectivos de biologia molecular. Objetivos: Comparar a quantidade e a qualidade do RNA extraido de amostras FFEP a partir de tres kits disponiveis comercialmente. MATERIAL E METODO: Utilizando-se tres diferentes procedimentos, o RNA total foi extraido de 14 blocos de parafina contendo fragmentos de carcinomas mamarios, todos arquivados ha 10 anos. A quantidade do RNA foi expressa em pg/µl; e a qualidade, pelo numero de integridade do RNA (NIR), utilizando-se o Bioanalyzer da Agilent com o Pico LabChip. O RNA de maior NIR extraido de cada uma das 14 amostras foi amplificado por reacao em cadeia da polimerase com transcricao reversa (RT-PCR) utilizando-se o gene G6PD, com primers designados para gerar fragmentos de 67, 151 e 242 pares de bases (pb). RESULTADOS: A media e a mediana da quantidade do RNA extraido para os tres protocolos foram, respectivamente, 42,91 e 31,31 pg/µl. A media e a mediana do NIR foram, respectivamente, 1,8 e 2. Em todas as amostras, o gene G6PD foi amplificado para fragmentos de RNA de 67 e 151 pb. DISCUSSAO: Como houve grande variacao individual na quantidade e na qualidade do RNA extraido para cada amostra, os dados do presente estudo indicam que, se nao for possivel extrair RNA de uma determinada amostra na primeira tentativa, uma segunda extracao deve ser realizada antes de se descartar essa amostra para testes de biologia molecular. CONCLUSOES: Nos tres procedimentos utilizados foi possivel extrair RNA de qualidade aceitavel para amplificacao por RT-PCR (com NIR > 1,4).
Family history and the risk of colorectal cancer: The importance of patients' history of colonoscopy

Registry‐based studies on the risk of colorectal cancer (CRC) for persons with a family history (FH) typically did not control for important covariates, such as history of colonoscopy. We aimed to quantify the association between FH and CRC risk, carefully accounting for potential confounders. We conducted a population‐based case–control study in Germany. A total of 4,313 patients with a first diagnosis of CRC (cases) and 3,153 controls recruited from 2003 to 2014 were included. We used multiple logistic regression analyses to assess the association between FH and risk of CRC with odds ratios (OR) and the resulting 95% confidence intervals (95% CI). A total of 582 cases (13.5%) and 321 (10.2%) controls reported a history of CRC in a first‐degree relative, which was associated with a 41% increase in risk of CRC (OR: 1.41, 95% CI 1.22–1.63) after adjustment for sex and age. The OR substantially increased to 1.73 (95% CI, 1.48–2.03) after comprehensive adjustment including previous colonoscopies. Irrespective of their FH status, persons with history of colonoscopies had a lower CRC risk compared with persons without previous colonoscopies and without family history (OR: 0.25, 95% CI, 0.22–0.28 for persons without FH and OR 0.45, 95% CI, 0.36–0.56 for persons with FH). In an era of widespread use of colonoscopy, adjusting for previous colonoscopy is therefore crucial for deriving valid estimates of FH‐related CRC risk. Colonoscopy reduces the risk of CRC among those with FH far below levels of people with no FH and no colonoscopy.
Inflammation and Cognition in Older Adults: Evidence from Taiwan

ABSTRACT Inflammation has been linked to clinical cognitive impairment, including Alzheimer’s disease. Less is known, however, about the relationship between inflammation and normal, age-associated cognitive decline. An understanding of the determinants of all types of cognitive decline is important for improving quality of life in an aging world. This study investigated whether biomarkers of inflammation were associated with cognitive function and decline in older Taiwanese adults. Data were from the Taiwan Longitudinal Study of Aging and the Social Environment and Biomarkers of Aging Study. Inflammation was measured in 2000 and 2006 as C-reactive protein, interleukin-6, soluble e-selectin, soluble intercellular adhesion molecule-1, and white blood cell count. Cognition was assessed by 10 cognitive and memory tasks, measured in 2006, 2007, and 2011. Growth curve models were used to examine the relationship between inflammation and cognitive score over this time period. Higher levels of inflammation were associated with lower baseline cognitive scores, but not with longitudinal change in cognitive score. This study did not support a causal link between inflammation and cognitive decline among this older cohort. The observed cross-sectional relationship could reflect a causal relationship that arises earlier in life, or confounding; additional research across the life course is warranted.
GSTP1 Ile105Val Polymorphism in Serbian Patients with Pancreatic Diseases

GSTP1 Ile105Val Polymorphism in Serbian Patients with Pancreatic Diseases The aim of the current preliminary case-control study was to identify glutathione S-transferase P1 (GSTP1) Ile105Val allele and genotype frequency and to evaluate its impact on susceptibility to pancreatic diseases in a Serbian population. This study has encompassed 157 patients with three major types of chronic pancreatic pathology: 47 with pancreatic cancer, 50 with chronic pancreatitis and 60 with type 2 diabetes mellitus, as well as 107 healthy individuals. The presence of GSTP1 Ile105Val polymorphism was analyzed using a PCR-RFLP method. Allele 105Val was less frequent in patients with pancreatic cancer (24.5%) and chronic pancreatitis (24.0%) and slightly more frequent in patients with type 2 diabetes mellitus (31.7%) in comparison to healthy individuals (29.9%), but the differences were not statistically significant. Distribution of Ile105Val polymorphism genotypes differed between the analyzed groups, but differences were also not statistically significant. There are only a few studies regarding the role of GSTP1 Ile105Val polymorphism in pancreatic diseases and their results are inconsistent. The significance of GSTP1 Ile105Val polymorphism for pancreatic pathology remains unclear and further studies are needed in order to elucidate its role in pancreatic diseases. Polimorfizam GSTP1 Ile105Val u Srpskoj Populaciji sa Pankreasnim Oboljenjima Cilj ove studije bio je da se odredi učestalost polimorfizma Ile105Val u genu za glutation S-transferazu P1 (GSTP1) i proceni njegov uticaj na rizik za obolevanje od pankreasnih bolesti u srpskoj populaciji. Studija je obuhvatila 157 pacijenata sa najčešćim bolestima pankreasa: 47 sa karcinomom pankreasa, 50 sa hroničnim pankreatitisom i 60 sa dijabetes melitusom tipa 2, kao i 107 zdravih ispitanika. Prisustvo polimorfizma Ile105Val u genu za GSTP1 je analizirano metodom PCR-RFLP (Polymerase Chain Reaction - Restriction Fragment Length Polymorphism). Učestalost alela 105Val je bila niža kod pacijenata sa karcinomom pankreasa (24,5%) i hroničnim pankreatitisom (24,0%) i neznatno povišena kod pacijenata sa dijabetes melitusom tipa 2 (31,7%) u odnosu na učestalost kod zdravih ispitanika (29,9%), ali razlike nisu bile statistički značajne. Učestalost pojedinih genotipova polimorfizma Ile105Val se razlikovala među analiziranim grupama, ali razlike takođe nisu bile statistički značajne. Samo nekoliko studija se do sada bavilo ulogom GSTP1 Ile105Val polimorfizma u bolestima pankreasa i uglavnom su dale oprečne rezultate. Značaj GSTP1 Ile105Val polimorfizma za bolesti pankreasa još uvek nije razjašnjen i potrebna su dalja istraživanja da bi se ispitala njegova uloga u pankreasnom tkivu.
Plasma Renin Activity and Its Postnatal Development in Preterm Infants

Immunoassayable plasma renin activity (PRA) was measured in 16 healthy preterm infants of different gestational ages. A total of 52 measurements have been performed between the second week of life and the date of the expected term. PRA was found markedly increased in preterm infants and a highly significative negative correlation with postmenstrual age was proved.
Suicide in a single health district: Epidemiology, and involvement of psychiatric services

This study derives suicide statistics for Leicestershire for the 6—year period 1988–1993, and explores risk factors for those with current and previous psychiatric contacts. The Leicestershire Mortality Statistics were scrutinised for possible suicides. Verdicts were reviewed, with consideration of further information when available, and coded as 'definite suicide', 'probable suicide', 'suicide unlikely' and 'definitely not suicide'. For those coded as definite or probable suicide, psychiatric records were examined further. Deaths were coded as definite suicide in 420 cases and probable suicide in a further 46 cases, of these: 347 were males, and 119 were females; 160 had a history of current and previous psychiatric care; and 46 had contact with psychiatric services within 1 week of death, a further 24 within 4 weeks and 23 within the previous 3 months. For the purposes of research and audit, identification of suicides should not rely solely on coroners' verdicts; a wider definition based upon the probable explanation of death may be more appropriate. There were a variety of factors identified in the records of suicides with psychiatric contacts indicating high risk. Improved service provision and practices may have a preventative role.
Quality of Life of Patients with Chronic Fatigue Syndrome

AbstractThe purpose of this study was to compare quality of life between patients with Chronic Fatigue Syndrome (CFS; n = 73) and healthy controls (n = 147), using a broad and generic quality of life assessment instrument, the World Health Organization Quality of Life assessment (WHOQOL-100). Participants were assessed on the WHOQOL-100, a self-assessment instrument designed for quantifying 24 facets relating to quality of life. These facets are grouped into six larger domains: physical health, psychological health, level of independence, social relationships, environment, and spirituality. The WHOQOL-100 also includes one facet examining overall quality of life and general health perceptions. Analyses revealed that the CFS group reported significantly lower levels of quality of life than the control group on overall quality of life and general health perceptions and on 22 out of the 24 facets of quality of life. Compared to earlier studies that used health-status scales or rather limited quality of life .
State of Art of Managing Pain in Patients With Cancer

AbstractPain in cancer patients involves complex interactions between physiological, psychological, sociocultural, sensory, cognitive, and behavioral dimensions. Pain management interventions will be most effective when pharmacological and nonpharmacological treatments are individualized after exploring the various contributors to pain and suffering, and the patient and family are educated and involved in decision making. This entails a systematic multidimensional approach with frequent reassessments of pain and related outcomes.
Rotavirus vaccine response correlates with the infant gut microbiota composition in Pakistan

ABSTRACT Rotavirus (RV) is the leading cause of diarrhea-related death in children worldwide and ninety-five percent of rotavirus deaths occur in Africa and Asia. Rotavirus vaccines (RVV) can dramatically reduce RV deaths, but have low efficacy in low-income settings where they are most needed. The intestinal microbiome may contribute to this decreased RVV efficacy. This pilot study hypothesizes that infants' intestinal microbiota composition correlates with RVV immune responses and that RVV responders have different gut microbiota as compared to non-responders. We conducted a nested, matched case-control study comparing the pre-vaccination intestinal microbiota composition between 10 6-week old Pakistani RVV-responders, 10 6-week old Pakistani RVV non-responders, and 10 healthy Dutch infants. RVV response was defined as an Immunoglobulin A of ≥20 IU/mL following Rotarix™(RV1) vaccination in an infant with a pre-vaccination IgA<20. Infants were matched in a 1:1 ratio using ranked variables: RV1 dosing schedule (6/10/14; 6/10; or 10/14 weeks), RV season, delivery mode, delivery place, breastfeeding practices, age and gender. Fecal microbiota analysis was performed using a highly reproducible phylogenetic microarray. RV1 response correlated with a higher relative abundance of bacteria belonging to Clostridium cluster XI and Proteobacteria, including bacteria related to Serratia and Escherichia coli. Remarkably, abundance of these Proteobacteria was also significantly higher in Dutch infants when compared to RV1-non-responders in Pakistan. This small but carefully matched study showed the intestinal microbiota composition to correlate with RV1 seroconversion in Pakistan infants, identifying signatures shared with healthy Dutch infants.
A polymicrobial view of disease potential in Crohn's-associated adherent-invasive E. coli

ABSTRACT The human gut is home to trillions of bacteria and provides the scaffold for one of the most complex microbial ecosystems in nature. Inflammatory bowel diseases, such as Crohn's disease, involve a compositional shift in the microbial constituents of this ecosystem with a marked expansion of Enterobacteriaceae, particularly Escherichia coli. Adherent-invasive E. coli (AIEC) strains are frequently isolated from the biopsies of Crohn's patients, where their ability to elicit inflammation suggests a possible role in Crohn's pathology. Here, we consider the origins of the AIEC pathovar and discuss how risk factors associated with Crohn's disease might influence AIEC colonization dynamics within the host to alter the overall disease potential of the microbial community.
Differential HPV16 variant distribution in squamous cell carcinoma, adenocarcinoma and adenosquamous cell carcinoma

Human Papillomavirus 16 (HPV16) causes 70% of invasive cervical cancers (ICC) worldwide. Interaction between HPV16 genetic diversity, host genetics and target tissue largely determine the chances to trigger carcinogenesis. We have analyzed the differential prevalence of viral variants in 233 HPV16‐monoinfected squamous (SCC), glandular (ADC) and mixed (ADSC) ICCs from four continents, assessing the contribution of geographical origin and cancer histology. We have further quantified the contribution of viral variants and cancer histology to differences in age at tumor diagnosis. The model fitted to the data explained 97% of the total variance: the largest explanatory factors were differential abundance among HPV16 variants (78%) and their interaction with cancer histology (9.2%) and geography (10.1%). HPV16_A1‐3 variants were more prevalent in SCC while HPV16_D variants were increased in glandular ICCs. We confirm further a non‐random geographical structure of the viral variants distribution. ADCs were diagnosed at younger ages than SCCs, independently of the viral variant triggering carcinogenesis. HPV16 variants are differentially associated with histological ICCs types, and ADCs are systematically diagnosed in younger women. Our results have implications for the implementation of cervical cancer screening algorithms, to ensure proper early detection of elusive ADCs.
Modulation of the gut microbiota by metformin improves metabolic profiles in aged obese mice

ABSTRACT The gut microbiota is a contributing factor in obesity-related metabolic disorders. The effect of metformin on the gut microbiota has been reported; however, the relationship between the gut microbiota and the mechanism of action of metformin in elderly individuals is unclear. In this study, the effect of metformin on the gut microbiota was investigated in aged obese mice. The abundance of the genera Akkermansia, Bacteroides, Butyricimonas, and Parabacteroides was significantly increased by metformin in mice fed a high-fat diet. Metformin treatment decreased the expression of IL-1β and IL-6 in epididymal fat, which was correlated with the abundance of various bacterial genera. In addition, both fecal microbiota transplantation from metformin-treated mice and extracellular vesicles of Akkermansia muciniphila improved the body weight and lipid profiles of the mice. Our findings suggest that modulation of the gut microbiota by metformin results in metabolic improvements in aged mice, and that these effects are associated with inflammatory immune responses.
The impact of tropomyosins on actin filament assembly is isoform specific

Abstract Tropomyosin (Tpm) is an α helical coiled-coil dimer that forms a co-polymer along the actin filament. Tpm is involved in the regulation of actin's interaction with binding proteins as well as stabilization of the actin filament and its assembly kinetics. Recent studies show that multiple Tpm isoforms also define the functional properties of distinct actin filament populations within a cell. Subtle structural variations within well conserved Tpm isoforms are the key to their functional specificity. Therefore, we purified and characterized a comprehensive set of 8 Tpm isoforms (Tpm1.1, Tpm1.12, Tpm1.6, Tpm1.7, Tpm1.8, Tpm2.1, Tpm3.1, and Tpm4.2), using well-established actin co-sedimentation and pyrene fluorescence polymerization assays. We observed that the apparent affinity (Kd(app)) to filamentous actin varied in all Tpm isoforms between ∼0.1–5 μM with similar values for both, skeletal and cytoskeletal actin filaments. The data did not indicate any correlation between affinity and size of Tpm molecules, however high molecular weight (HMW) isoforms Tpm1.1, Tpm1.6, Tpm1.7 and Tpm2.1, showed ∼3-fold higher cooperativity compared to low molecular weight (LMW) isoforms Tpm1.12, Tpm1.8, Tpm3.1, and Tpm4.2. The rate of actin filament elongation in the presence of Tpm2.1 increased, while all other isoforms decreased the elongation rate by 27–85 %. Our study shows that the biochemical properties of Tpm isoforms are finely tuned and depend on sequence variations in alternatively spliced regions of Tpm molecules.
Insights into the Initiation of Eukaryotic DNA Replication

The initiation of DNA replication is a highly regulated event in eukaryotic cells to ensure that the entire genome is copied once and only once during S phase. The primary target of cellular regulation of eukaryotic DNA replication initiation is the assembly and activation of the replication fork helicase, the 11-subunit assembly that unwinds DNA at a replication fork. The replication fork helicase, called CMG for Cdc45-Mcm2–7, and GINS, assembles in S phase from the constituent Cdc45, Mcm2–7, and GINS proteins. The assembly and activation of the CMG replication fork helicase during S phase is governed by 2 S-phase specific kinases, CDK and DDK. CDK stimulates the interaction between Sld2, Sld3, and Dpb11, 3 initiation factors that are each required for the initiation of DNA replication. DDK, on the other hand, phosphorylates the Mcm2, Mcm4, and Mcm6 subunits of the Mcm2–7 complex. Sld3 recruits Cdc45 to Mcm2–7 in a manner that depends on DDK, and recent work suggests that Sld3 binds directly to Mcm2–7 and also to single-stranded DNA. Furthermore, recent work demonstrates that Sld3 and its human homolog Treslin substantially stimulate DDK phosphorylation of Mcm2. These data suggest that the initiation factor Sld3/Treslin coordinates the assembly and activation of the eukaryotic replication fork helicase by recruiting Cdc45 to Mcm2–7, stimulating DDK phosphorylation of Mcm2, and binding directly to single-stranded DNA as the origin is melted.
Beyond Tethering and the LEM domain: MSCellaneous functions of the inner nuclear membrane Lem2

ABSTRACT The nuclear envelope plays a pivotal role in the functional organization of chromatin. Various inner nuclear membrane (INM) proteins associate with transcriptionally repressed chromatin, which is often found at the nuclear periphery. A prominent example is the conserved family of LEM (LAP2-Emerin-MAN1) domain proteins that interact with DNA-binding proteins and have been proposed to mediate tethering of chromatin to the nuclear membrane. We recently reported that the fission yeast protein Lem2, a homolog of metazoan LEM proteins, contributes to perinuclear localization and silencing of heterochromatin.1 We demonstrate that binding and tethering of centromeric chromatin depends on the LEM domain of Lem2. Unexpectedly, this domain is dispensable for heterochromatin silencing, which is instead mediated by a different structural domain of Lem2, the MSC (MAN1-Src1 C-terminal) domain. Hence, silencing and tethering by Lem2 can be mechanistically separated. Notably, the MSC domain has multiple functions beyond heterochromatic silencing. Here we discuss the implications of these novel findings for the understanding of this conserved INM protein.