Miracle-dz/UniFAR-FTUs huggingface dataset:
MicroRNA-137 promoter methylation as an etiologic and prognostic biomarker for squamous cell carcinoma of the head and neck

Head and neck cancer accounted for 3.3% of incident malignancies and 2.0% of cancer-deaths in the US in 2009, the majority of which are squamous in origin. Thus, there is a need for novel biomarkers for early detection and prognosis of squamous cell carcinoma of the head and neck (SCCHN). MicroRNA-137 plays a role in cell cycle control through negative regulation of Cdk6, and has been reported to undergo promoter methylation in oral squamous cell carcinoma. Oral rinse is a non-invasive mode of DNA collection, which may have some utility in detection of promoter methylation. The primary goals of this research were to determine if miR-137 promoter methylation occurs in all SCCHN, including pharyngeal and laryngeal tumors, and whether it is detectable in oral rinse samples; and to assess miR-137 promoter methylation as an etiologic and prognostic biomarker for SCCHN. DNA was extracted from oral rinses from 99 SCCHN patients and 99 cancer-free control subjects and from tumor tissue of 67 SCCHN patients; paired oral rinses and tumor tissue was available for 64 of the SCCHN patients. Promoter methylation status of miR-137 was determined by methylation-specific PCR. We identified a strong association between miR-137 promoter methylation detected in oral rinses and SCCHN (OR = 4.80, 95% CI: 1.23-18.82). There was a strong positive association between female gender and miR-137 promoter methylation in oral rinse from SCCHN patients (OR = 5.30, 95% CI: 1.20-23.44) and an inverse association with body mass index (OR = 0.88, 95% CI: 0.77-0.99). Promoter methylation of miR-137 in tumor tissue was associated with poorer overall survival (HR = 3.68, 95% CI: 1.01-13.38). In spite of its low sensitivity (21.2%), miR-137 methylation detected in oral rinse may have future value in methylation panels for early diagnosis of SCCHN due to its high specificity (97.0%) and occurrence in early stage disease; and its detection in tumor tissue has promise as a prognostic marker. The identification of novel diagnostic and prognostic biomarkers for SCCHN such as miR-137 promoter methylation will significantly impact public health through the reduction of morbidity and mortality that occurs as a result of this disease.
Social organization in European small mustelids

Abstract A review of the social organization in the weasel ( Mustela nivalis ) and stoat ( M. erminea ) is made, based mainly on my earlier mark-recapture studies on weasels and stoats and radio-tracking studies on stoats. During the non-breeding season, from September to April, the small mustelids are organized in a territorial pattern; individuals of the same sex exploit exclusive areas. The extensive male territories often include one or several female ranges. The territories are probably delineated mainly by scent marking. During the breeding season the males increase their movement activity and extend their ranges. The territorial systems brake down and male ranges generally overlap considerably. Depending on their social status, males adopt different strategies, i.c. roaming or staying, in their attempts to obtain as many matings as possible. Prey abundance and distribution are considered to be the decisive factors determining female spacing behaviour throughout the year. The great amount of food required by females when rearing young makes it rewarding to defend and use restricted areas exclusively. In males there is a seasonal change in social organization resulting from a shift in decisive resources; i.e. priority is placed on procuring receptive females during the breeding and food during the non-breeding season. Riassunto Organizzazione sociale nei piccoli mustelidi europei - L'autore presenta un'analisi dell'organizzazione sociale della donnola ( Mustela nivalis ) e dell'ermellino ( M. erminea ), basata soprattutto sui suoi studi effettuati mediante i metodi di marcamento-ricattura per entrambe le specie e di radio-telemetria per l'ermellino. Durante la stagione non riproduttiva, da settembre ad aprile, i piccoli mustelidi sono organizzati secondo un modello territoriale: individui dello stesso sesso utilizzano aree esclusive. Gli ampi territori dei maschi spesso includono quello di una o piu femmine. Probabilmente i territori sono delimitati principalmente con marcamenti odorosi (feci). Durante la stagione riproduttiva i maschi incrementano i loro movimenti e estendono le loro aree vitali. Il sistema territoriale non viene piu mantenuto e le aree vitali dei maschi generalmente si sovrappongono notevolmente. In relazione al loro stato sociale, i maschi adottano differenti strategie: cioe, vagano o restano nella loro area vitale nel tentativo di avere piu accoppiamenti possibile. La distribuzione e l'abbondanza delle prede sono considerati i fattori prioritari che determinano il comportamento spaziale delle femmine nell'arco dell'anno. L'elevata richiesta di cibo da parte delle femmine durante l'allevamento della prole si traduce nella difesa ed uso esclusivo di aree limitate. L'organizzazione sociale dei maschi varia stagionalmente in relazione al cambiamento delle risorse di "vitale importanza": durante la stagione riproduttiva diventa prioritario procurarsi femmine recettive, mentre durante quella non riproduttiva diventa fondamentale il cibo.
{2-[(1,3-Benzothiazol-2-yl)methoxy]-5-chlorophenyl}(4-chlorophenyl)methanone

In the title compound, C21H13Cl2NO2S, the benzothiazole ring makes dihedral angles of 0.94 (1) and 70.65 (5)° with the 4-chlorophenylmethanone unit and the 5-chlorophenyl ring, respectively. The dihedral angle between the 4-chlorophenylmethanone unit and the 5-chlorophenyl ring is 66.20 (5)°. The crystal structure consists of dimeric units generated by C—H⋯N hydrogen bonds, further linked by C—H⋯O and C—H⋯π interactions, leading to a three-dimensional network.
Oogenesis and steroid profiles during the reproductive cycle of female angelfish Pterophyllum scalare (Cichlidae)

The changes in oogenesis and sex hormones during the reproductive cycle of the multi-spawning, synchronic angelfish, Pterophyllum scalare , were studied. The average cycle lasts 11 days, during which the oocytes pass through vitellogenesis to maturation before spawning occurs. Six major stages of the oocytes during oogenesis are described. The patterns of steroid changes were traced by high pressure liquid chromatography and by radioimmunoassay. The levels of the main steroids 17P-estradiol (E^) and testosterone (T), rose during vitellogenesis while 17a, 20P, dihydroxy-4-pregnen-3-one was very low and did not change markedly. The levels of E^ and T increased significantly in the plasma by an injection of carp pituitary extract which also led to a higher percentage of oocytes in maturation than was found in the control group.
[(Z)-N-(3-Chlorophenyl)-O-ethylthiocarbamato-κS](triphenylphosphine-κP)gold(I)

The title compound, [Au(C9H9ClNOS)(C18H15P)], reveals a near linear geometry for the Au atom defined by a S,P-donor set [S—Au—P = 175.86 (3)°]. The deviation from linearity is ascribed to the proximate O atom derived from the thiocarbamato anion [Au⋯O = 2.967 (3) Å].
Nanoparticles for hyperthermic therapy: synthesis strategies and applications in glioblastoma

Glioblastoma multiforme (GBM) is the most common and most aggressive malignant primary brain tumor in humans. Current GBM treatment includes surgery, radiation therapy, and chemotherapy, sometimes supplemented with novel therapies. Despite recent advances, survival of GBM patients remains poor. Major challenges in GBM treatment are drug delivery across the blood–brain barrier, restriction of damage to healthy brain tissues, and limitation of resistance to therapies. This article reviews recent advances in the application of magnetic nanoparticles (MNPs), gold nanorods (GNRs), and carbon nanotubes (CNTs) for hyperthermia ablation of GBM. First, the article introduces GBM, its current treatment, and hyperthermia as a potential modality for the management of GBM. Second, it introduces MNPs, GNRs, and CNTs as inorganic agents to induce hyperthermia in GBM. Third, it discusses different methodologies for synthesis of each inorganic agent. Finally, it reviews in vitro and in vivo studies in which MNPs, GNRs, and CNTs have been applied for hyperthermia ablation and drug delivery in GBM.
Yaws

Yaws is a non-venereal endemic treponemal infection caused by Treponema pallidum sub-species pertenue, a spirochaete bacterium closely related to Treponema pallidum ssp. pallidum, the agent of venereal syphilis. Yaws is a chronic, relapsing disease predominantly affecting children living in certain tropical regions. It spreads by skin-to-skin contact and, like syphilis, occurs in distinct clinical stages. It causes lesions of the skin, mucous membranes and bones which, without treatment, can become chronic and destructive. Treponema pallidum ssp. pertenue, like its sexually-transmitted counterpart, is exquisitely sensitive to penicillin. Infection with yaws or syphilis results in reactive treponemal serology and there is no widely available test to distinguish between these infections. Thus, migration of people from yaws-endemic areas to developed countries may present clinicians with diagnostic dilemmas. We review the epidemiology, clinical presentation and treatment of yaws.
Periodization

Background: Clinicians are constantly faced with the challenge of designing training programs for injured and noninjured athletes that maximize healing and optimize performance. Periodization is a concept of systematic progression—that is, resistance training programs that follow predictable patterns of change in training variables. The strength training literature is abundant with studies comparing periodization schemes on uninjured, trained, and untrained athletes. The rehabilitation literature, however, is scarce with information about how to optimally design resistance training programs based on periodization principles for injured athletes. The purpose of this review is to discuss relevant training variables and methods of periodization, as well as periodization program outcomes. A secondary purpose is to provide an anecdotal framework regarding implementation of periodization principles into rehabilitation programs. Evidence Acquisition: A Medline search from 1979 to 2009 was implemented with the keywords periodization, strength training, rehabilitation, endurance, power, hypertrophy, and resistance training with the Boolean term AND in all possible combinations in the English language. Each author also undertook independent hand searching of article references used in this review. Results: Based on the studies researched, periodized strength training regimens demonstrate improved outcomes as compared to nonperiodized programs. Conclusions: Despite the evidence in the strength training literature supporting periodization programs, there is a considerable lack of data in the rehabilitation literature about program design and successful implementation of periodization into rehabilitation programs.
Acute Care Physical Therapy Intervention for a Patient who Presented Post-Op Right Total Hip and Right Total Knee Arthroplasty: A Case Report.

Study Design: Case report. Background: The incidence of patients undergoing a total hip or total knee arthroplasty is continually increasing. Despite this increase in prevalence, few studies have reported the outcomes of physical therapy (PT) intervention for a patient who has undergone a simultaneous ipsilateral total hip and total knee arthroplasty. The purpose of this retrospective case report is to describe the clinical, functional, and patient reported outcomes impacted by skilled PT intervention in the rehabilitation of a patient who presented to acute care PT immediately post-op simultaneous right total hip (postero-lateral approach) and right total knee arthroplasty. Case Description: The patient described within this retrospective case report was a 53-year-old Caucasian male who presented to acute care PT post-op day 1 after a simultaneous right total hip and right total knee arthroplasty. This patient had also undergone a simultaneous left total hip and left total knee arthroplasty within six months prior to this episode of care. Outcomes: Following two days of PT intervention, with two PT sessions per day, the patient demonstrated improvements in pain ratings, functional mobility, gait velocity, ambulation distance, stairs ascended, and active range of motion (AROM) of the right knee and right hip. Conclusion: PT intervention appeared to be correlated with improvements in functional and clinical outcomes for the patient described in this case report. Future research is needed to determine the long-term effects of PT intervention on clinical and functional outcomes for patients who have undergone a simultaneous ipsilateral total hip and total knee arthroplasty.
Nano technological drug release approaches for the treatment of eye diseases: Myth, reality or challenge?

Fil: Formica, Maria Lina. Universidad Nacional de Cordoba. Facultad de Ciencias Quimicas; Argentina. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Cordoba. Unidad de Investigacion y Desarrollo en Tecnologia Farmaceutica. Universidad Nacional de Cordoba. Facultad de Ciencias Quimicas. Unidad de Investigacion y Desarrollo en Tecnologia Farmaceutica; Argentina
Characterization Of Bacteriophages From Environmental Water Samples And The Potential Of Bacteriophages Tailspike Proteins (tsp) In Bacteria Detection

ABSTRACT CHARACTERIZATION OF BACTERIOPHAGES FROM ENVIRONMENTAL WATER SAMPLES AND THE POTENTIAL OF BACTERIOPHAGES TAILSPIKE PROTEINS (TSP) IN BACTERIA DETECTION by GAYATHRI UPEKSHA GUNATHILAKA May 2014 Advisor: Dr. Yifan Zhang Major: Nutrition and Food Science Degree: Master of Science The high abundance of phage in the environment and their specificity with the bacteria host make them an excellent tool for bacteria detection. To characterize phage specific to Salmonella and E. coli from water samples in the Southeastern Michigan and to develop a novel bacterial detection method using phage, environmental water samples were collected from rivers and waste water treatment plant (WWTP) in Southeastern Michigan. E. coli and Salmonella phage were isolated from water samples using soft agar overlay technique with multiple indicator strains. Host range of phage was determined using 18 Salmonella strains and 14 E. coli strains. Transmission Electron Microscopy (TEM) was used to visualize the morphology of representative phage. Tailspike Protein (TSP) purified from E. coli O157 phage ФV10 was functionalized on a graphene field-effect-transister (FET). The specificity of TSP and E. coli O157 binding was measured by the shift of Dirac Point. A total of 70 Salmonella phage and 33 E. coli phage were purified. Twelve E. coli phages were able to grow in all 4 E. coli O157 strains tested. Out of 37 host range patterns in Salmonella phage, all the patterns were able to multiply in 3 strains and above. Out of 9 host range patterns observed in E. coli phage, 6 were able to multiply in 3 strains and above. This suggests a broad host range of the phage recovered. According to the TEM pictures, all of the E. coli phages and some of Salmonella phages were tailed phages. Detectable conductance change was observed when E. coli O157 binds to TSP-functionalized graphene FET whereas very small shift in Dirac Point was caused by Salmonella binding, indicating high specificity of E. coli O157 interaction with TSP. In conclusion, phage with broad host ranges is prevalent in water. Phage has the potential to be applied to bacteria detection.
A 1961-90 climatology for Africa south of the Equator and a comparison of potential evapotranspiration estimates

A 1961-90 mean monthly climatology for Africa south of the Equator was constructed at a resolution of 0.5° latitude/longitude for a suite of eight surface climate variables: minimum, maximum and mean air temperature; rainfall; sunshine hours; vapour pressure; wind speed; and rain day (>0.1 mm)frequencies. This climatology was constructed from observed station data distributed across the region with station frequencies ranging from 288 (wind speed) to 916 (rainfall). Over 92% of these data is based on observations between 1961-90 and over 85% has been supplied by national meteorological agencies from the region. Additionally, for mean temperature and rainfall, monthly anomalies with respect to the 1961-90 average have been calculated at the same spatial resolution for each month from January 1961 to December 1994. This paper describes the dataset which has been compiled for this work, the interpolation methods which have been used, together with some assessment of the accuracy of the resulting climate surfaces. The interpolation of the 1961-90 normals uses elevation, as well as longitude and latitude, as predictor variables and this enables three climate surfaces to be constructed for each variable, reflecting the 'minimum', mean and 'maximum' elevation within each 0.5° cell. The interpolation of the anomaly fields uses a simpler method in which elevation is not considered. These anomaly time series enable fields of interannual variability to be established for mean temperature and rainfall. The second part of the paper uses this climatology to construct fields of mean monthly potential evapotranspiration (PET) for the region using a number of different calculation methods. A comparison of the resulting PET estimates highlights significant spatial and seasonal biases due to differences in climate input variables and in the theoretical representation of PET. The climatology, described and analysed here is available from the authors for use in climate modelling and the study of climate change in Africa south of the Equator.
A new method of protein extraction from red wines

Aim: Wine is a very complex medium and is often evaluated according to its main components like alcohol, sugar, tannins, and acid levels. Proteins are rarely considered in this evaluation because their concentrations are only a few mg/L of wine. However, in an enological context, proteins appear to be more and more important, in particular for the stability of wines with protein haze problems. The study of proteins is less obvious in red wines than in white wines because the proteins are strongly tied to tannins, which makes their extraction and analysis even more difficult.Methods and results: This article describes a technique for the separation of proteins from tannins thanks to a methanol/chloroform emulsion in an acid solution. The protein extract, obtained after 4 hours, was later analyzed by SDS-Page and the protein profile of the wine established. Experiments showed that the protein profiles remained the same during the different stages of the winemaking process, whereas the overall amount of proteins decreased. Characteristic protein profiles of different grape varieties were established, and it was also possible to visualize the presence of exogenous proteins from fining agents like albumin and casein.Conclusion: This procedure allowed the extraction of proteins from 8 red wine samples within 4 hours. It also made it possible to analyze the extracted proteins by SDS-Page without tannin interference within 2 hours.Significance and impact of the study: This method shows in a very promising manner how proteins might be extracted from red wines after being separated from their tannins. The extracted proteins are then available for analysis using even more advanced techniques such as ESI-QTof or ELISA.
Ecological Divergence Among Extremely Close Relatives in Bacillus

vi Chapter 1: Introduction . 1 1.1 Bacterial Genetics and Reproduction 2 1.2 Bacterial Species 6 1.3 Ecotype Theory 11 1.4 Algorithms for Identifying Ecotypes 18 1.5 Ecological Homogeneity within Ecotypes 22 1.6 Full Genome Studies: Genome Content Comparisons 24 1.7 Study System, Selection of Isolates 26 Chapter 2: Genome Content Comparison of Extremely Close Relatives in Bacillus . 30 2.1 The Foundational Study: An Overview 31 2.2 Sequencing, Annotation, and Analysis 33 2.3 Bacillus subtilis Complex Phylogeny 35 2.4 Core Genome Phylogeny 35 2.5 Genome Content Comparisons 38 Chapter 3: Ecological Resolution of Genomic Heterogeneity . 44 3.1 Foundational Study Legacy and Current Study Aims 45 3.2 Metabolic Pathways of Interest 48 3.2.1 Maltose/Maltodextrin Utilization 49 3.2.2 L-rhamnose Uptake and Utilization 52 3.2.2 myo-Inositol Uptake and Utilization 54 Chapter 4: Methods . 56 4.1 Utility of RFW Isolates 57 4.2 Minimal Media: Selection and Composition 58 4.3 Monoculture Experiments 60 4.4 Competition Experiments 61
Innate immune responses in HIV-1 infected macrophages

In this study M-CSF differentiated human monocyte derived macrophages were used to investigate HIV-1 interactions with macrophage innate immune responses. Macrophages may be an important host cell for HIV-1. HIV-1 can infect and replicate within these cells without causing host cell cytopathicity unlike in T cells. Macrophages also aid in the spread of the virus and are likely to act as a viral reservoir protected from antivirals and immune responses due to the unique localisation of the virus within these cells. Surprisingly HIV-1 infection has little effect on the steady state transcriptome of MDM and despite the role of macrophages to detect incoming pathogens; no innate immune response to HIV-1 could be detected, in contrast with other viruses tested. The lack of immune response was not due to active viral suppression and addition of exogenous IFN or activation of the innate immune response at the time of HIV-1 infection can restrict viral infection in these cells, despite HIV-1 having a full complement of accessory proteins known to counteract IFN inducible restriction factors. This HIV-1 restriction induced by IFN was long lasting, likely for the lifetime of the MDM. IFN treatment of MDM with established HIV-1 infection however only transiently suppressed viral replication. Comparisons of MDM with other cell types which do show an innate immune IFN response to HIV-1 showed that MDM have relatively low levels of TLR7 gene expression, suggesting that MDM may lack one of the PRRs for detecting HIV-1. HIV-1 infection of MDM was found to attenuate NFκB activation in response to TLR stimulation and this attenuation could be reversed by priming the MDM with IFNγ. However this attenuation of the NFκB signal did not translate into decreased protein expression for a selection of proinflammatory cytokines examined.
A Hybrid Model for Automatic Emotion Recognition in Suicide Notes

We describe the Open University team's submission to the 2011 i2b2/VA/Cincinnati Medical Natural Language Processing Challenge, Track 2 Shared Task for sentiment analysis in suicide notes. This Shared Task focused on the development of automatic systems that identify, at the sentence level, affective text of 15 specific emotions from suicide notes. We propose a hybrid model that incorporates a number of natural language processing techniques, including lexicon-based keyword spotting, CRF-based emotion cue identification, and machine learning-based emotion classification. The results generated by different techniques are integrated using different vote-based merging strategies. The automated system performed well against the manually-annotated gold standard, and achieved encouraging results with a micro-averaged F-measure score of 61.39% in textual emotion recognition, which was ranked 1st place out of 24 participant teams in this challenge. The results demonstrate that effective emotion recognition by an automated system is possible when a large annotated corpus is available.