Learning what to read: Focused machine reading

Recent efforts in bioinformatics have achieved tremendous progress in the machine reading of biomedical literature, and the assembly of the extracted biochemical interactions into large-scale models such as protein signaling pathways. However, batch machine reading of literature at today's scale (PubMed alone indexes over 1 million papers per year) is unfeasible due to both cost and processing overhead. In this work, we introduce a focused reading approach to guide the machine reading of biomedical literature towards what literature should be read to answer a biomedical query as efficiently as possible. We introduce a family of algorithms for focused reading, including an intuitive, strong baseline, and a second approach which uses a reinforcement learning (RL) framework that learns when to explore (widen the search) or exploit (narrow it). We demonstrate that the RL approach is capable of answering more queries than the baseline, while being more efficient, i.e., reading fewer documents.Comment: 6 pages, 1 figure, 1 algorithm, 2 tables, accepted to EMNLP 201

Controlling Correlated Tunneling and Superexchange Interactions with AC-Driven Optical Lattices

The dynamical control of tunneling processes of single particles plays a major role in science ranging from Shapiro steps in Josephson junctions to the control of chemical reactions via light in molecules. Here we show how such control can be extended to the regime of strongly interacting particles. Through a weak modulation of a biased tunnel contact, we have been able to coherently control single particle and correlated two-particle hopping processes. We have furthermore been able to extend this control to superexchange spin interactions in the presence of a magnetic-field gradient. We show how such photon assisted superexchange processes constitute a novel approach to realize arbitrary XXZ spin models in ultracold quantum gases, where transverse and Ising type spin couplings can be fully controlled in magnitude and sign.Comment: 10 pages, 9 figure

Experimental realization of plaquette resonating valence bond states with ultracold atoms in optical superlattices

The concept of valence bond resonance plays a fundamental role in the theory of the chemical bond and is believed to lie at the heart of many-body quantum physical phenomena. Here we show direct experimental evidence of a time-resolved valence bond quantum resonance with ultracold bosonic atoms in an optical lattice. By means of a superlattice structure we create a three-dimensional array of independent four-site plaquettes, which we can fully control and manipulate in parallel. Moreover, we show how small-scale plaquette resonating valence bond states with s- and d-wave symmetry can be created and characterized. We anticipate our findings to open the path towards the creation and analysis of many-body RVB states in ultracold atomic gases.Comment: 7 page, 4 figures in main text, 3 figures in appendi

A canine model of irreversible urethral sphincter insufficiency

OBJECTIVE To develop a canine model of external urinary sphincter insufficiency by creating irreversible damage to the sphincter, because there is a need for a reliable and reproducible large animal model for the study of stress urinary incontinence (SUI) caused by deficient sphincter function. MATERIALS AND METHODS About a quarter of the total external sphincter muscle was removed microsurgically from seven female dogs; three age-matched dogs served as normal controls. The dogs had standard urodynamic and radiographic studies before and at 1, 2, 3, 4 and 7 months after surgery. Three dogs were killed at 4 months and four at 7 months after surgery for tissue analyses. RESULTS The interventions produced a consistent outcome. Urodynamic studies showed a significant and sustained decrease in sphincter function, which included a static urethral pressure profile, stress urethral profile and detrusor leak-point pressure. Furthermore, in vivo pudendal nerve stimulation and organ-bath studies of the retrieved tissue strips confirmed the loss of sphincter tissue function. Histologically, absence of functional sphincter muscle was evident in the damaged sphincter region. CONCLUSIONS These results show that a reliable and reproducible canine model of irreversible sphincter insufficiency can be created by microsurgical removal of sphincter muscle tissue. This model of external sphincter insufficiency could be used for evaluating methods (e.g. cell therapies) for treating SUI

Like-Triple Diabetes as First Manifestation of MODY2 in an Overweight Teenager With Transient Multiple Antibodies. Diabetes Care 2014; 37: e66-e67

Ctr Referencia Estadual Assistencia Ao Diabet & E, Salvador, BA, BrazilUniversidade Federal de São Paulo, Ctr Diabet, São Paulo, BrazilUniversidade Federal de São Paulo, Ctr Diabet, São Paulo, BrazilWeb of Scienc

Controle glicêmico em pacientes adultos com diabetes do tipo 1 em uma cidade brasileira: comparação entre abordagem multidisciplinar e endocrinológica de rotina

OBJECTIVE: To evaluate the metabolic control of a cohort of adult type 1 diabetes mellitus (T1DM) patients assisted in a public Diabetes Center (DC) that follows the rules of a national diabetes society. METHODS: We compared for one year the metabolic control and the characteristics of 175 T1DM patients attended by a multidisciplinary team in a DC (test group) with 30 patients assisted only by endocrinologists at a public endocrinology outpatient center (control group). RESULTS: The test group presented a larger proportion of well-controlled patients (p= 0.002). The proportions (test x control group) were as follows: 51.4% x 16.7% in the subgroup with A1C 8%. Patients assisted in the DC presented a likelihood 4.38 times higher of reaching levels of A1C up to 7%. CONCLUSIONS: This study shows the effectiveness of a DC and emphasizes the importance of education, adherence and multidisciplinarity as cornerstones for the treatment, showing that in developing countries it is possible to treat T1DM with satisfactory results.OBJETIVO: Avaliar o controle metabólico de uma coorte de pacientes adultos com diabetes do tipo 1 (DM1) atendidos em um Centro de Diabetes (CD) que segue as normas da Sociedade Brasileira de Diabetes. MÉTODOS: Foram comparados o controle glicêmico e as características de 175 pacientes com DM1 atendidos por uma equipe multidisciplinar em um CD (grupo teste) com 30 pacientes assistidos em um ambulatório de endocrinologia geral (grupo controle) durante um ano. RESULTADOS: O grupo teste apresentou uma maior proporção de pacientes bem controlados (p= 0,002). As proporções (grupo teste x grupo controle) foram: 51,4% x 16,7% no subgrupo com A1C 8%. Os pacientes atendidos no CD apresentaram probabilidade 4,38 vezes maior de atingir níveis de A1C até 7%. CONCLUSÃO: O estudo mostra a efetividade do CD e enfatiza a importância da educação, aderência e da multidisciplinaridade como pedras angulares do tratamento, mostrando ser possível tratar o DM1 nos países em desenvolvimento com resultados satisfatórios.Universidade Federal de São Paulo (UNIFESP)Universidade Federal de Juiz de Fora Departamento de FisiologiaUNIFESPSciEL

A Noninvasive Test for Vesico-Ureteric Reflux in Children

Objective To report the development and testing of a device for the noninvasive diagnosis of vesico‐ureteric reflux (VUR) which avoids the need for urethral catheterization (currently required to reliably determine the presence of VUR), and which thus avoids the anxiety of parents and patients that causes many families to refuse such evaluation. Patients and methods Fifty‐four children (49 girls and five boys, mean age 7.2 years, range 4–14) previously evaluated as having VUR volunteered to participate; no child was symptomatic at the time of the study. Refluxing units were known to be present by voiding cysto‐urethrography (within 1 year, mean 7 months) in 45 and absent in 16. The device developed acquires electronically processed acoustic signals from the child during an observed urination. The signals are then analysed ‘off‐line’ to determine the presence or absence of VUR. The initial preparation for the test included: (i) a full bladder [at least 0.80 × {(2+age) ×30 mL}] measured by ultrasonography; and (ii) localization of the pelvi‐ureteric junction by ultrasonography to accurately place the device\u27s sensors on the child\u27s back. The children were then positioned at a commode after placing the sensors; the recording was started and continued until voiding occurred. The children were tested with the recording and analysis team unaware of the presence and/or degree of VUR. The first 47 studies were single‐kidney examinations and the remaining seven included simultaneous monitoring of both kidneys. Results Sixty‐one renal units were assessed and interpretable signals were obtained from 54 (89%). There were seven episodes of ‘system failure’ when no interpretable data were obtained. One unit with no VUR had a ‘reflux’ signal; in four kidneys, spontaneous (two) and postsurgical (two) resolution of reflux was predicted by the testing and subsequently verified by cyclic radionuclide cystography. Conclusions This noninvasive diagnostic technique detected VUR in 35 of 37 refluxing units and verified no reflux in 16 of 17 units without VUR. Further refinements may allow this technology to be used in all children with suspected VUR

GeneChip analysis of human embryonic stem cell differentiation into hemangioblasts: an in silico dissection of mixed phenotypes

Transcriptional profiling of human embryonic stem cells differentiating into blast cells reveals that erythroblasts are the predominant cell type in the blast cell population. In silico comparisons with publicly available data sets revealed the presence of endothelia, cardiomyocytes and hematopoietic lineages

Bilayered constructs aimed at osteochondral strategies : the influence of media supplements in the osteogenic and chondrogenic differentiation of amniotic fluid-derived stem cells

injuries and aging associated diseases that affect joints. This study reports the development of a bilayered scaffold, which consists of both bone and cartilage regions. On the other hand, amniotic fluid-derived stem cells (AFSCs) could be differentiated into either osteogenic or chondrogenic cells, respectively. In this study we have developed a bilayered scaffolding system, which includes a starch/polycaprolactone (SPCL) scaffold for osteogenesis and an agarose hydrogel for chondrogenesis. AFSC-seeded scaffolds were cultured for 1 or 2 weeks in an osteochondral-defined culture medium containing both osteogenic and chondrogenic differentiation factors. Additionally, the effect of the presence or absence of insulin-like growth factor-1 (IGF-1) in the culture medium was assessed. Cell viability and phenotypic expression were assessed within the constructs in order to determine the influence of the osteochondral differentiation medium. The results indicated that, after osteogenic differentiation, AFSCs that had been seeded onto SPCL scaffolds did not require osteochondral medium to maintain their phenotype, and they produced a protein-rich, mineralized extracellular matrix (ECM) for up to 2 weeks. However, AFSCs differentiated into chondrocyte-like cells appeared to require osteochondral medium, but not IGF-1, to synthesize ECM proteins and maintain the chondrogenic phenotype. Thus, although IGF-1 was not essential for creating osteochondral constructs with AFSCs in this study, the osteochondral supplements used appear to be important to generate cartilage in long-term tissue engineering approaches for osteochondral interfaces. In addition, constructs generated from agarose–SPCL bilayered scaffolds containing pre-differentiated AFSCs may be useful for potential applications in regeneration strategies for damaged or diseased joints.Fundação para a Ciência e a Tecnologia (FCT