Miracle-dz/UniFAR-FTUs huggingface dataset:
MLH1 germline epimutations in selected patients with early‐onset non‐polyposis colorectal cancer

Recently, the germline epigenetic inactivation of MLH1 has been reported in a number of patients with early‐onset colorectal cancer among other characteristics. The aim of the present study is to evaluate the presence of MLH1 germline epimutations in selected colorectal cancer patients suspected of hereditary non‐polyposis colorectal cancer (HNPCC) in order to determine in which patients the MLH1 epigenetic test should be performed. From a total of 109 microsatellite instability (MSI)‐positive HNPCC‐suspected patients, 11 showed a lack of MLH1 expression in tumor tissue and no germline mutations in the mismatch repair (MMR) genes. In nine of these cases and in three additional patients with multiple tumors, the study of the germline MLH1 promoter hypermethylation was performed by means of methylation‐specific PCR and combined bisulfite‐restriction analysis techniques. One of the selected patients resulted positive for the MLH1 epimutation, which was confirmed in the DNA extracted from buccal lavage. The patient with the epimutation had developed an epidermoid lip carcinoma and an early‐onset colorectal tumor with MSI, no MLH1 expression, and loss of heterozygosity of the gene. Parents and siblings did not carry the epigenetic alteration, suggesting a de novo mechanism. Although germline MLH1 epimutations seem to be mostly uncommon, when the cases are well selected, the probability of finding them increases. Thus, taking into account ours and previous reports, we propose that screening for MLH1 epimutations in blood DNA could be performed in early‐onset colorectal cancer patients with MSI, lack of MLH1 expression in the tumor, and no germline mutations in the MMR genes.
Role of cellular design in bacterial metal accumulation and mineralization.

L'accumulation des metaux par les bacteries: article de synthese. Morphologie des bacteries. Surfaces bacteriennes. Necessite de la presence d'ions metalliques pour les surfaces bacteriennes. Sorption des metaux a la surface des bacteries, precipitation, developpement des mineraux. Depots internes de metal. Ubiquite et âge des procaryotes. Microbiogeochimie
[Syndromic autism: II. Genetic syndromes associated with autism].

INTRODUCTION AND DEVELOPMENT In this study we report on the different genetic syndromes in which autism has been described as one of the possible manifestations. CONCLUSIONS Certain genetic syndromes are providing us with extremely valuable information about the role played by genetics in autism. This is the case of the following syndromes: Angelman syndrome, Prader-Willi syndrome, 15q11-q13 duplication, fragile X syndrome, fragile X premutation, deletion of chromosome 2q, XYY syndrome, Smith-Lemli-Opitz syndrome, Apert syndrome, mutations in the ARX gene, De Lange syndrome, Smith-Magenis syndrome, Williams syndrome, Rett syndrome, Noonan syndrome, Down syndrome, velo-cardio-facial syndrome, myotonic dystrophy, Steinert disease, tuberous sclerosis, Duchenne's disease, Timothy syndrome, 10p terminal deletion, Cowden syndrome, 45,X/46,XY mosaicism, Myhre syndrome, Sotos syndrome, Cohen syndrome, Goldenhar syndrome, Joubert syndrome, Lujan-Fryns syndrome, Moebius syndrome, hypomelanosis of Ito, neurofibromatosis type 1, CHARGE syndrome and HEADD syndrome.
Antibody-coated gold nanoparticles immunoassay for direct detection of Aeromonas salmonicida in fish tissues.

Aeromonas salmonicida is the causative agent of furunculosis, a disease that affects both salmonid and non-salmonid fish. Detection of A. salmonicida can be labour intensive and time consuming because of the difficulties in distinguishing the bacterium from other species given the wide variety of existing biochemical profiles and the slow growth characteristics which allow other organisms to overgrow the A. salmonicida. Herein, we report the development of a specific immunoassay using gold-conjugated polyclonal antibodies for the rapid detection of A. salmonicida in fish tissues. Monodispersible 13-nm gold nanoparticles were coated with polyclonal antibodies specific to A. salmonicida. Reddish purple agglutination of gold particles indicated the presence of A. salmonicida in samples. Positive reactions were detected visually with the naked eye. No agglutination was observed when A. salmonicida antibody-coated gold nanoparticles were tested with other common bacterial fish pathogens, thereby verifying the specificity of the assay. The assay could detect A. salmonicida in fish tissues down to 1 × 10(4) CFU mL(-1) , and results were obtained within 45 min. The antibody-coated gold nanoparticles were stable for at least 2 months at 4 ° C. The immunoassay using antibody-coated gold nanoparticles represents a promising tool for the rapid and specific detection of A. salmonicida in fish tissues.
Untersuchungen von Nanostrukturen magnetischer Kolloide mit Kleinwinkelstreuung

The small angle neutron scattering with polarised neutrons was used for an analysis of various magnetic colloids, the so-called ferrofluids. Ferrofluids are dispersions of magnetisable particles which are mostly protected against an irreversible aggregation by organic shells. Using diluted magnetite colloid solutions, dextrane, tensides (laurine acid/marlipal) and electrostatically stabilised magnetite particles were analysed. It was found that each of the fluids consisted of two sorts of particles, i.e. aggregates and core-shell-particles. In the electrostatically stabilized sample the aggregates only consisted of magnetite. In the other two cases the aggregates also contained shell material. The surfactant stabilised ferrofluid contained even a third fraction of particles of non-magnetic tenside structures. Especially for the surfactant stabilised samples the influence of the solvent becomes obvious. It will be shown that in the case of toluol as solvent a single surfactant layer is built. In water there was a double layer present. Additionally, the radius of the aggregates proved to be larger in a higher deuterated solvent and at a higher dilution, independently from the kind of solvent. The different core materials were compared using a magnetite and a Cobalt sample. Apart from size differences to magnetite caused by preparation, no aggregates could be found in the Cobalt fluid. Surfactant structures appeared here like those found in magnetite fluid. Concentrated Cobalt ferrofluids showed structure formation phenomena in external magnetic fields. Two concurrent structures could be verified. First, chain formations appeared along the the magnetic field. Otherwise planes of hexagonal order with [110]-direction formed along the external magnetic field. The causation of the hexagonal order could not be completely clarified and needs further experimental and theoretical investigations.
Endoscopic Methods in the Diagnosis and Treatment of Pancreatic Cancer

Endoscopic methods are widely used in the diagnosis and palliative treatment of pancreatic cancer. The most sensitive method in early diagnosis is endosonography (EUS) which can also provide histological diagnosis. Diagnostic ERCP became a rather rare procedure as a consequence of wide availability of Magnetic Resonance Cholangiopancreatography (MRCP) but ERCP assisted intraductal methods have gained importance (brush-cytology, intraductal ultrasound, optical coherence tomography) and finally, peroral pancreatoscopy has become technically feasible but available only in some specialized centers. Minimally invasive endoscopic methods play an important role in the palliative treatment of unresectable pancreatic cancer which represents the majority of cases. EUS-guided histological confirmation of adenocarcinoma is crucial in the election of chemotherapy. Celiac plexus blockade and endoscopic biliary and pancreatic stent placement contribute to pain reduction, drainage of obstructed bile duct and assure a better quality of life.
Pycoevol - A Python Workflow to Study Protein-protein Coevolution

Protein coevolution has emerged as an important research topic. Several methods and scoring systems were developed to quantify coevolution, though the quality of the results usually depends on the completeness of the biological data. To simplify the computation of coevolution indicators from the data, we have implemented a fully integrated and automated workflow which enables efficient analysis of protein coevolution, using the Python scripting language. Pycoevol automates access to remote or local databases and third-party applications, including also data processing functions. For a given protein complex under study, Pycoevol retrieves and processes all the information needed to undergo the analysis, namely homologous sequence search, multiple sequence alignment computation and coevolution analysis, using a Mutual Information indicator. In addition, friendly output results are created, namely histograms and heatmaps of inter-protein mutual information scores, as well as lists of significant coevolving residue pairs. An illustrative example is presented. Pycoevol is platform independent, and is available under the general public license from http://code.google. com/p/pycoevol.
The impact of prenatal alcohol exposure on frontal cortex development in utero.

OBJECTIVE Whether prenatal alcohol exposure was associated with a reduction in the frontal cortex was examined. STUDY DESIGN Pregnant women (n = 167) received multiple ultrasonographic assessments. During the assessment, brain structures were visualized and measured, including the distance from the posterior margin of the cavum to the calvarium, the distance from the posterior margin of the thalamus to the calvarium, the transcerebellar diameter, and the biparietal diameter. RESULTS Regression analyses and odds ratios demonstrated that alcohol exposure was associated with a reduction in the frontal cortex, but not other brain structures. Strikingly, the percent of fetuses with a frontal cortex below the 10th percentile increased from 4% for nonexposed fetuses to 23% for heavily exposed fetuses. CONCLUSION There was a relationship between frontal brain size and maternal alcohol consumption, suggesting that ultrasonography may be a sensitive tool for detecting alcohol-induced changes in the fetal brain.
Anthrax: A Re-Emerging Livestock Disease

Anthrax is a contagious and highly fatal zoonotic bacterial disease affecting primarily herbivores. Mortality can be very high, especially in herbivores. The disease has world-wide distribution and is a zoonosis. The etiological agent is the endospore-forming, Gram-positive, nonmotile, rod-shaped Bacillus anthracis. Central to the persistence of anthrax in an area is the ability of B. anthracis to form long-lasting, highly resistant spores. Understanding the ecology of anthrax spores is essential if one hopes to control epidemics. Studies on the ecology of anthrax spores have found a correlation between the disease and specific soil factors, such as alkaline pH, high moisture, and high organic content. The repeated anthrax outbreak in livestock and subsequent infection to human has been considered as a nationwide alarming issue. Outbreaks of anthrax have diverse consequences on society. Establishing the appropriate control strategies is very important and crucial in reducing the socio-economic impact of the disease. Control measures are aimed at breaking the cycle of infection, and their implementation must be adhered to rigorously. It can be used as a biological weapon and has been classified as a Category ‘A’ bio threat by Centers for Disease Control and Prevention (CDC). This review describes this important disease covering its etiology, epidemiology, transmission, pathogenesis, clinical signs, diagnosis and prevention and control strategies to be adopted to combat this globally important pathogen.
Collaborating with consumers: the key to achieving statutory notification for birth defects and cerebral palsy in Western Australia.

INTRODUCTION The Western Australian Birth Defects Registry and the Western Australian Cerebral Palsy Register used multiple sources of voluntary notification without consent and have a high level of case ascertainment, but there were concerns over privacy and a call for statutory notification. OBJECTIVE To seek consumer consensus on whether notification to the registers should be statutory or only with consent. METHODS Two facilitated workshops for consumer and community members of groups representing people with birth defects, cerebral palsy and disability, and the Western Australian Health Consumers' Council. RESULTS Parent groups and the Health Consumers' Council were unanimous in their support for statutory notification, with 3 conditions: that comprehensive and open information be provided to consumer groups and community; that consumers have input into the development of statutory notification; and that an opt-out clause be included. A Consumer Reference Group was established. They decided on a name for the new register (Western Australian Register of Developmental Anomalies), developed an opt-out clause and reviewed drafts of the regulations for statutory notification. The regulations came into effect in January 2011. CONCLUSIONS Consumers were key to achieving statutory notification. We encourage others to engage with their consumers and community in equal partnership for mutual benefit.
Learning in Reinforcement Learning

Transfer learning in reinforcement learning is an area of research that seeks to speed up or improve learning of a complex target task, by leveraging knowledge from one or more source tasks. This thesis will extend the concept of transfer learning to curriculum learning, where the goal is to design a sequence of source tasks for an agent to train on, such that final performance or learning speed is improved. We discuss completed work on this topic, including methods for semi-automatically generating source tasks tailored to an agent and the characteristics of a target domain, and automatically sequencing such tasks into a curriculum. Finally, we also present ideas for future work.
Convolution engine

General-purpose processors, while tremendously versatile, pay a huge cost for their flexibility by wasting over 99% of the energy in programmability overheads. We observe that reducing this waste requires tuning data storage and compute structures and their connectivity to the data-flow and data-locality patterns in the algorithms. Hence, by backing off from full programmability and instead targeting key data-flow patterns used in a domain, we can create efficient engines that can be programmed and reused across a wide range of applications within that domain. We present the Convolution Engine (CE)---a programmable processor specialized for the convolution-like data-flow prevalent in computational photography, computer vision, and video processing. The CE achieves energy efficiency by capturing data-reuse patterns, eliminating data transfer overheads, and enabling a large number of operations per memory access. We demonstrate that the CE is within a factor of 2--3× of the energy and area efficiency of custom units optimized for a single kernel. The CE improves energy and area efficiency by 8--15× over data-parallel Single Instruction Multiple Data (SIMD) engines for most image processing applications.
The impact of family history on ovarian cancer risk. The Utah Population Database.

OBJECTIVE To estimate the relative risks and population attributable risks of ovarian cancer associated with family histories of cancer at several sites. METHODS A matched case-control analytic study (662 cases, 2647 controls), employing the Utah Population Database, a genealogy of approximately 1 million individuals linked to cancer incidence data from the Utah Cancer Registry. Family history was assessed using kinship order and a kinship-weighted familial standardized incidence ratio statistic. RESULTS Family histories of ovarian, uterine, breast, and pancreatic cancer were significantly associated with increased risk of ovarian cancer. The relative risk of ovarian cancer was 4.31 (95% confidence interval [CI], 2.35 to 7.90) for women with a first-degree relative with ovarian cancer, 2.12 (95% CI, 1.19 to 3.78) for women with an affected second-degree relative, and 1.48 (95% CI, 0.98 to 2.24) for women with an affected third-degree relative. The odds ratio (OR) was 2.06 (95% CI, 1.44 to 2.93) for those with the highest familial standardized incidence ratio. No age differences were observed between cases with and without a family history of ovarian cancer. There was substantial heterogeneity of family history effects by cell type. Increased parity was not protective among women with a strong family history of cancer at the sites studied (OR, 1.11; 95% CI, 0.38 to 3.26), although it was protective among women without a family history of these cancers (OR, 0.29; 95% CI, 0.11 to 0.62). CONCLUSIONS The risk of ovarian cancer was substantially increased among women with family histories of ovarian, uterine, pancreatic, and, to a lesser degree, breast cancer. Among women with family histories of any of these cancers, the risk of ovarian cancer is not diminished by high parity.
Proteomic analysis of the sarcosine‐insoluble outer membrane fraction of the bacterial pathogen Bartonella henselae

Bartonella henselae is an emerging zoonotic pathogen causing a wide range of disease manifestations in humans. In this study, we report on the analysis of the sarcosine‐insoluble outer membrane fraction of B. henselae ATCC 49882 Houston‐1 by one‐dimensional sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (1‐D SDS‐PAGE) and two‐dimensional nonequilibrium pH gradient polyacrylamide gel electrophoresis (2‐D NEPHGE). Protein species were identified by matrix‐assisted laser desorption/ionization‐time of flight‐mass spectrometry (MALDI‐TOF‐MS) and subsequent database query against the B. henselae genome sequence. Subcellular fractionation, application of the ionic detergent lauryl sarcosine, assessment of trypsin sensitivity, and heat modifiability of surface‐exposed proteins represented valuable tools for the analysis of the outer membrane subproteome of B. henselae. 2‐D NEPHGE was applied to display and catalogue a substantial number of proteins associated with the B. henselae sarcosine‐insoluble outer membrane fraction, resulting in the establishment of a first 2‐D reference map of this compartment. Thus, 53 distinct protein species associated with the outer membrane subproteome fraction were identified. This study provides novel insights into the membrane biology and the associated putative virulence factors of this pathogen of increasing medical importance.
The Hunt For The Kill Switch

This paper has described the issues on electronic circuits which are made for military equipments.The DoD of U.S. recently launched its most ambitious program yet to verify the integrity of the electronics that will underpin future additions to its arsenal. The Defense Advanced Research Projects Agency (DARPA), the Pentagon's R&D wing, and released details about a three-year initiative it calls the Trust in Integrated Circuits program. The findings from the program could give the military and defense contractors who make sensitive microelectronics like the weapons systems for the F-35 a guaranteed method of determining whether their chips have been compromised. The Trust program started its prequalifying rounds by sending to three contractors four identical versions of a chip that contained unspecified malicious circuitry, though U.S. military consumes only 1% of world's integrated circuits.
In Vitro Osteogenesis of Synovium Mesenchymal Cells Induced by Controlled Release of Alendronate and Dexamethasone from a Sintered Microspherical Scaffold

In vitro osteogenesis was successfully achieved with synovium-derived mesenchymal stem cells (SMSCs), which intrinsically have a strong chondrogenic tendency, by in situ release of alendronate (AL) and dexamethasone (Dex) from poly(lactic-co-glycolic acid) (PLGA)/hydroxyapatite (HA) sintered microspherical scaffold (PLGA/HA-SMS). Cumulative release profiles of AL and Dex from PLGA/HA-SMS and the influence on SMSCs osteogenic commitment were investigated. SMSCs seeded in Al-/Dex-loaded PLGA/HA-SMS (PLGA/HA-Com-SMS) exhibited significant osteogenic differentiation, as indicated by high yields of alkaline phosphatase (ALP) and bone calcification. In addition, mechanical properties (compressional) of PLGA/HA-Com-SMSs were also evaluated and approved. In conclusion, by promoting osteogenic commitment of SMSCs in vitro, this newly designed controlled-release system opens a new door to bone reparation and regeneration.
The Plastid and Mitochondrial Peptidase Network in Arabidopsis thaliana: A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis

Plant plastids and mitochondria have dynamic proteomes. Protein homeostasis in these organelles is maintained by a proteostasis network containing protein chaperones, peptidases, and their substrate recognition factors. However, many peptidases, as well as their functional connections and substrates, are poorly characterized. This review provides a systematic insight into the organellar peptidase network in Arabidopsis thaliana. We present a compendium of known and putative Arabidopsis peptidases and inhibitors, and compare the distribution of plastid and mitochondrial peptidases to the total peptidase complement. This comparison shows striking biases, such as the (near) absence of cysteine and aspartic peptidases and peptidase inhibitors, whereas other peptidase families were exclusively organellar; reasons for such biases are discussed. A genome-wide mRNA-based coexpression data set was generated based on quality controlled and normalized public data, and used to infer additional plastid peptidases and to generate a coexpression network for 97 organellar peptidase baits (1742 genes, making 2544 edges). The graphical network includes 10 modules with specialized/enriched functions, such as mitochondrial protein maturation, thermotolerance, senescence, or enriched subcellular locations such as the thylakoid lumen or chloroplast envelope. The peptidase compendium, including the autophagy and proteosomal systems, and the annotation based on the MEROPS nomenclature of peptidase clans and families, is incorporated into the Plant Proteome Database.
Diet effects on enterocyte development

Enterocytes produced in intestinal crypts express a genetically determined programme of development during migration towards the tips of villi which is also influenced by environmental factors such as diet. Delayed weaning, for instance, reduces the amount of sucrase (EC 3.2.1.48) appearing in the small intestine (Henning, 1985) and changing the diet of adult animals affects the ability of enterocytes to absorb amino acids (Dauncey et al. 1983; King et al. 1983; Cremaschi et al. 1986). A major difficulty encountered in analysing these effects arises, however, from the fact that dietary change often affects crypt cell proliferation, either by altering the level of luminal nutrition or by changing the rate at which pancreaticobiliary secretions appear in the gut (Dowling, 1982). Use of isoenergetic diets will not control this variable when the substituted component is poorly metabolized (Smith et al. 1990~). Routine measurement of proliferative status (Al-Mukhtar et al. 1981) and enterocyte turnover (Leblond, 1991) should be carried out whenever possible to eliminate or quantify possible trophic effects of diet on intestinal function. Enterocytes change their structure and their ability to digest and absorb nutrients during maturation, and differentiation of some of these properties takes place sequentially in fetal as well as adult intestine (see Smith, 1985, 1991). Modern techniques of immunocytochemistry (Shields et al. 1986; Sweetser et al. 1988) enzyme cytochemistry (Gossrau, 1980; James et al. 1988; Tivey & Smith, 1989), autoradiography (King et al. 1983; Smith et al. 1983) and in situ hybridization (Boller et al. 1988; Kiyama et al. 1991) now make it possible to assess quantitatively how diet affects the expression of these different functions in villus-attached enterocytes.