LLukas22/scidocs huggingface dataset:
A system for modelling cell-cell interactions during plant morphogenesis.

BACKGROUND AND AIMS
During the development of multicellular organisms, cells are capable of interacting with each other through a range of biological and physical mechanisms. A description of these networks of cell-cell interactions is essential for an understanding of how cellular activity is co-ordinated in regionalized functional entities such as tissues or organs. The difficulty of experimenting on living tissues has been a major limitation to describing such systems, and computer modelling appears particularly helpful to characterize the behaviour of multicellular systems. The experimental difficulties inherent to the multitude of parallel interactions that underlie cellular morphogenesis have led to the need for computer models.


METHODS
A new generic model of plant cellular morphogenesis is described that expresses interactions amongst cellular entities explicitly: the plant is described as a multi-scale structure, and interactions between distinct entities is established through a topological neighbourhood. Tissues are represented as 2D biphasic systems where the cell wall responds to turgor pressure through a viscous yielding of the cell wall.


KEY RESULTS
This principle was used in the development of the CellModeller software, a generic tool dedicated to the analysis and modelling of plant morphogenesis. The system was applied to three contrasting study cases illustrating genetic, hormonal and mechanical factors involved in plant morphogenesis.


CONCLUSIONS
Plant morphogenesis is fundamentally a cellular process and the CellModeller software, through its underlying generic model, provides an advanced research tool to analyse coupled physical and biological morphogenetic mechanisms.
Introducing ethics and engineering: the case of Delft University of Technology

This article focuses mainly on (1) the policy of Delft University of Technology since 1992 as regards the university-wide introduction of a compulsory course on ethics and engineering, and (2) the ideal structure of such a course, including the educational goals of the course.
A Pattern Language - Towns, Buildings, Construction

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SPEAKER IDENTIFICATION USING MEL FREQUENCY CEPSTRAL COEFFICIENTS

This paper presents a security system based on speaker identification. Mel frequency Cepstral Coefficients{MFCCs} have been used for feature extraction and vector quantization technique is used to minimize the amount of data to be handled .
Lean Semantic Interpretation

We introduce two abstraction mechanisms for streamlining the process of semantic interpretation. Configurational descriptions of dependency graphs increase the linguistic generality of interpretation schemata, while interfacing them to lexical and conceptual inheritance hierarchies reduces the amount and complexity of semantic specifications.
Ventilator-induced lung injury, cytokines, PEEP, and mortality: implications for practice and for clinical trials

A mainstay in the supportive care of patients with acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) is mechanical ventilation. However, a number of animal and clinical studies have demonstrated that mechanical ventilation itself can worsen preexisting lung injury and produce ventilator-induced lung injury (VILI). Although the most obvious clinical abnormalities of ALI/ARDS are related to lung function, the most common cause of death is dysfunction of other organs, termed multiple organ dysfunction syndrome (MODS) [1], which is commonly accompanied by the systemic inflammatory response syndrome (SIRS). SIRS/MODS is a complex syndrome, often precipitated and intensified by a series of events rather than a single event. Recent clinical trials have demonstrated that in patients with ARDS, protective ventilatory strategies are associated with decreased serum cytokine levels [2, 3], decreased levels of organ dysfunction [3, 4], and decreased mortality [3, 5], perhaps by partially mitigating the development of MODS [6]. There are a number of factors that can precipitate the development of ALI/ARDS, including sepsis, shock, trauma, and aspiration of gastric contents. Among these sepsis is the leading cause and the major contributor to mortality in most ICUs [1, 7, 8]. Thus investigation of the impact of ventilatory strategy in the context of sepsis is of great interest. In their contribution to Intensive Care Medicine Herrera and colleagues [9] take a molecular approach to the study of VILI, systemic inflammatory cytokines, and mortality using an in vivo rat sepsis model produced by cecal ligation and perforation. They found that the application of positive end-expiratory pressure (PEEP) above the lower inflection point (LIP) of the respiratory system pressure-volume curve decreased pulmonary and systemic inflammatory cytokines [tumor necrosis factor (TNF) α and interleukin (IL) 6] as well as mortality in septic animals ventilated with low tidal volume (VT; 6 ml/kg), but when higher PEEP levels were applied with high VT (20 ml/kg), cytokines and mortality increased. The strengths of the study are the use of a clinically relevant injury model of sepsis and the use of multiple endpoints including mortality. However, it would have been interesting to have had data on the effect of the ventilatory strategies on hemodynamics, especially with large VT and PEEP. Mechanical ventilation, in particular application of PEEP and use of large VT, can have detrimental effects on systemic and regional hemodynamics as well as on global oxygen delivery and consumption, as highlighted in many excellent reviews [10, 11, 12]. It is likely that the use of high tidal volumes in conjunction with the high PEEP levels led to significant hemodynamic consequences and contributed to the mortality in this group.
Obesity in children and young people: a crisis in public health.

Ten per cent of the world’s school-aged children are estimated to be carrying excess body fat (Fig. 1), with an increased risk for developing chronic disease. Of these overweight children, a quarter are obese, with a significant likelihood of some having multiple risk factors for type 2 diabetes, heart disease and a variety of other co-morbidities before or during early adulthood. The prevalence of overweight is dramatically higher in economically developed regions, but is rising significantly in most parts of the world. In many countries the problem of childhood obesity is worsening at a dramatic rate. Surveys during the 1990s show that in Brazil and the USA, an additional 0.5% of the entire child population became overweight each year. In Canada, Australia and parts of Europe the rates were higher, with an additional 1% of all children becoming overweight each year. The burden upon the health services cannot yet be estimated. Although childhood obesity brings a number of additional problems in its train – hyperinsulinaemia, poor glucose tolerance and a raised risk of type 2 diabetes, hypertension, sleep apnoea, social exclusion and depression – the greatest health problems will be seen in the next generation of adults as the present childhood obesity epidemic passes through to adulthood. Greatly increased rates of heart disease, diabetes, certain cancers, gall bladder disease, osteoarthritis, endocrine disorders and other obesityrelated conditions will be found in young adult populations, and their need for medical treatment may last for their remaining life-times. The costs to the health services, the losses to society and the burdens carried by the individuals involved will be great. The present report has been written to focus attention on the issue and to urge policy-makers to consider taking action before it is too late. Specifically, the report:
The ADDITION-Cambridge trial protocol: a cluster – randomised controlled trial of screening for type 2 diabetes and intensive treatment for screen-detected patients

BACKGROUND
The increasing prevalence of type 2 diabetes poses a major public health challenge. Population-based screening and early treatment for type 2 diabetes could reduce this growing burden. However, the benefits of such a strategy remain uncertain.


METHODS AND DESIGN
The ADDITION-Cambridge study aims to evaluate the effectiveness and cost-effectiveness of (i) a stepwise screening strategy for type 2 diabetes; and (ii) intensive multifactorial treatment for people with screen-detected diabetes in primary care. 63 practices in the East Anglia region participated. Three undertook the pilot study, 33 were allocated to three groups: no screening (control), screening followed by intensive treatment (IT) and screening plus routine care (RC) in an unbalanced (1:3:3) randomisation. The remaining 27 practices were randomly allocated to IT and RC. A risk score incorporating routine practice data was used to identify people aged 40-69 years at high-risk of undiagnosed diabetes. In the screening practices, high-risk individuals were invited to take part in a stepwise screening programme. In the IT group, diabetes treatment is optimised through guidelines, target-led multifactorial treatment, audit, feedback, and academic detailing for practice teams, alongside provision of educational materials for newly diagnosed participants. Primary endpoints are modelled cardiovascular risk at one year, and cardiovascular mortality and morbidity at five years after diagnosis of diabetes. Secondary endpoints include all-cause mortality, development of renal and visual impairment, peripheral neuropathy, health service costs, self-reported quality of life, functional status and health utility. Impact of the screening programme at the population level is also assessed through measures of mortality, cardiovascular morbidity, health status and health service use among high-risk individuals.


DISCUSSION
ADDITION-Cambridge is conducted in a defined high-risk group accessible through primary care. It addresses the feasibility of population-based screening for diabetes, as well as the benefits and costs of screening and intensive multifactorial treatment early in the disease trajectory. The intensive treatment algorithm is based on evidence from studies including individuals with clinically diagnosed diabetes and the education materials are informed by psychological theory. ADDITION-Cambridge will provide timely evidence concerning the benefits of early intensive treatment and will inform policy decisions concerning screening for type 2 diabetes.


TRIAL REGISTRATION
Current Controlled trials ISRCTN86769081.
Sit-to-stand tests for COPD: A literature review.

BACKGROUND
Sit-to-stand tests (STST) have recently been developed as easy-to-use field tests to evaluate exercise tolerance in COPD patients. As several modalities of the test exist, this review presents a synthesis of the advantages and limitations of these tools with the objective of helping health professionals to identify the STST modality most appropriate for their patients.


METHOD
Seventeen original articles dealing with STST in COPD patients have been identified and analysed including eleven on 1min-STST and four other versions of the test (ranging from 5 to 10 repetitions and from 30 s to 3 min). In these studies the results obtained in sit-to-stand tests and the recorded physiological variables have been correlated with the results reported in other functional tests.


RESULTS
A good set of correlations was achieved between STST performances and the results reported in other functional tests, as well as quality of life scores and prognostic index. According to the different STST versions the processes involved in performance are different and consistent with more or less pronounced associations with various physical qualities. These tests are easy to use in a home environment, with excellent metrological properties and responsiveness to pulmonary rehabilitation, even though repetition of the same movement remains a fragmented and restrictive approach to overall physical evaluation.


CONCLUSIONS
The STST appears to be a relevant and valid tool to assess functional status in COPD patients. While all versions of STST have been tested in COPD patients, they should not be considered as equivalent or interchangeable.
Persistent Nonalcoholic Fatty Liver Disease Increases Risk for Carotid Atherosclerosis.

BACKGROUND & AIMS
Nonalcoholic fatty liver disease (NAFLD) has been associated with subclinical atherosclerosis in cross-sectional studies. We investigated the longitudinal association of NAFLD with the development of subclinical carotid atherosclerosis.


METHODS
We performed a retrospective cohort study of 8020 adult men (average age, 49.2 y) without carotid atherosclerosis at baseline who underwent repeated health check-up examinations from January 1, 2005, through December 31, 2013. NAFLD status was diagnosed by ultrasonography and classified into 4 groups based on baseline and follow-up findings: none, developed, regressed, or persistent NAFLD. Subclinical carotid atherosclerosis was measured by ultrasound.


RESULTS
The age-adjusted hazard ratio for subclinical carotid atherosclerosis development comparing participants with persistent NAFLD with those without NAFLD was 1.23 (95% confidence interval [CI], 1.13-1.35; P < .001). The association persisted after adjustment for smoking, alcohol, body mass index, and weight change (hazard ratio, 1.13; 95% CI, 1.03-1.25; P = .014), but disappeared after adjustment for metabolic variables. The hazard ratio, comparing subjects with regression of NAFLD vs those with persistent NAFLD, was 0.82 (95% CI, 0.69-0.96; P = .013). The risk of subclinical carotid atherosclerosis development also was higher among participants with a high NAFLD fibrosis score, fibrosis-4 scores, or levels of γ-glutamyl transferase at baseline.


CONCLUSIONS
In a large cohort study, persistent NAFLD was associated with an increased risk of subclinical carotid atherosclerosis development. This association was explained by metabolic factors that could be potential mediators of the effect of NAFLD. Markers of liver fibrosis also were associated with subclinical carotid atherosclerosis development. Prospective studies are needed to determine whether treatment of NAFLD can reduce this risk.
Myosin IIA deficient cells migrate efficiently despite reduced traction forces at cell periphery

Cell motility is a cornerstone of embryogenesis, tissue remodeling and repair, and cancer cell invasion. It is generally thought that migrating cells grab and exert traction force onto the extracellular matrix in order to pull the cell body forward. While previous studies have shown that myosin II deficient cells migrate efficiently, whether these cells exert traction forces during cell migration in the absence of the major contractile machinery is currently unknown. Using an array of micron-sized pillars as a force sensor and shRNA specific to each myosin II isoform (A and B), we analyzed how myosin IIA and IIB individually regulate cell migration and traction force generation. Myosin IIA and IIB localized preferentially to the leading edge where traction force was greatest, and the trailing edge, respectively. When individual myosin II isoforms were depleted by shRNA, myosin IIA deficient cells lost actin stress fibers and focal adhesions, whereas myosin IIB deficient cells maintained similar actin organization and focal adhesions as wild-type cells. Interestingly, myosin IIA deficient cells migrated faster than wild-type or myosin IIB deficient cells on both a rigid surface and a pillar array, yet myosin IIA deficient cells exerted significantly less traction force at the leading edge than wild-type or myosin IIB deficient cells. These results suggest that, in the absence of myosin IIA mediated force-generating machinery, cells move with minimal traction forces at the cell periphery, thus demonstrating the remarkable ability of cells to adapt and migrate.
One-year multicentre outcomes of transapical aortic valve implantation using the SAPIEN XT™ valve: the PREVAIL transapical study.

OBJECTIVES
The study aimed to evaluate 1-year outcomes of the multicentre PREVAIL transapical (TA) study of TA-aortic valve implantation (AVI) in high-risk patients.


METHODS
From September 2009 to August 2010, a total of 150 patients, aged 81.6 ± 5.8 years, 40.7% female, were included at 12 European TA-AVI experienced sites. Patients received 23 (n = 36), 26 (n = 57) and 29 mm (n = 57) second-generation SAPIEN XT™ (Edwards Lifesciences, Irvine, CA, USA) valves. The mean logistic EuroSCORE was 24.3 ± 7.0, and mean Society Thoracic Surgeons score was 7.5 ± 4.4%.


RESULTS
Survival was 91.3% at 30 days and 77.9% at 1 year. Subgroup analysis revealed survivals of 91.7/88.9, 86.0/70.2, 96.55/91.2% for patients receiving 23-, 26- and 29-mm valves at 30 days and at 1 year, respectively. Transthoracic echocardiography revealed preserved left ventricular ejection fraction and low gradients. Aortic incompetence was none in 41/48, trace 30/36, mild 22/12 and moderate in 7/4% at discharge and 1 year. Walking distance increased from 221 (postimplant) to 284 m (at 1 year, P = 0.0004). Three patients required reoperation due to increasing aortic incompetence during follow-up. Causes of mortality at 1 year were cardiac (n = 7), stroke (n = 1) and others (n = 5).


CONCLUSIONS
The European PREVAIL multicentre trial demonstrates good functionality and good outcomes for TA-AVI using the second-generation SAPIEN XT prosthesis and the ASCENDRA-II delivery system. The 29-mm SAPIEN XT valve was successfully introduced and showed excellent results.
Few-fJ/bit data transmissions using directly modulated lambda-scale embedded active region photonic-crystal lasers

A low operating energy is needed for nanocavity lasers designed for on-chip photonic network applications. On-chip nanocavity lasers must be driven by current because they act as light sources driven by electronic circuits. Here, we report the high-speed direct modulation of a lambda-scale embedded active region photonic-crystal (LEAP) laser that holds three records for any type of laser operated at room temperature: a low threshold current of 4.8 mA, a modulation current efficiency of 2.0 GHz mA and an operating energy of 4.4 fJ bit. Five major technologies make this performance possible: a compact buried heterostructure, a photonic-crystal nanocavity, a lateral p–n junction realized by ion implantation and thermal diffusion, an InAlAs sacrificial layer and current-blocking trenches. We believe that an output power of 2.17 mW and an operating energy of 4.4 fJ bit will enable us to realize on-chip photonic networks in combination with the recently developed highly sensitive receivers.
Evaluation of the digital rectal examination as a screening test for prostate cancer. Rotterdam section of the European Randomized Study of Screening for Prostate Cancer.

BACKGROUND
The utility of digital rectal examination (DRE) as a screening test for early detection of prostate cancer has not been established. Therefore, we evaluated the usefulness of DRE as a stand-alone screening test and in conjunction with measured serum prostate-specific antigen (PSA) levels of 0-3.9 ng/mL and transrectal ultrasonography (TRUS).


METHODS
Our study population consisted of 10,523 men aged 54-76 years who were randomly assigned to the screening arm of the Rotterdam, The Netherlands, section of the European Randomized Study of Screening for Prostate Cancer. The underlying prevalence of detectable prostate cancer was estimated by logistic regression analysis and used for calculating the sensitivity of DRE as a test. Pathologic characteristics of 105 radical prostatectomy specimens were used to determine the aggressiveness of the tumors diagnosed (and missed) by DRE.


RESULTS
The overall detection rate for prostate cancer in this population when serum PSA measurement, DRE, and TRUS were used was 4.5%, and the detection rate with DRE alone was 2.5%. The positive predictive value of DRE ranged from 4% to 11% in men with PSA levels of 0-2.9 ng/mL and from 33% to 83% in men with PSA levels of 3.0-9.9 ng/mL or more. Most tumors detected by DRE in men with PSA levels of less than 4.0 ng/mL were small (mean volumes = 0.24-0.83 mL), and most were well differentiated (Gleason scores of 6 or less). Minimal, moderate, and advanced cancers were seen in 42%, 42%, and 16% of men, respectively, with a PSA level of 4.0 ng/mL or less. DRE alone allowed detection of 264 (55.8%) of 473 cancers; 82 (17.3%) of the 473 cancers would have remained undetected by PSA-based screening alone (i.e., no follow-up procedures for PSA values of 0-3.9 ng/mL).


CONCLUSIONS
For PSA values of 0-3.9 ng/mL, the positive predictive value and sensitivity of DRE, tumor volume, and tumor grade were strongly dependent on PSA level. DRE has a poor performance in low PSA ranges.
Ethnicity and pathways to care during first episode psychosis: the role of cultural illness attributions

BACKGROUND
Studies demonstrate ethnic variations in pathways to care during first episode psychosis (FEP). There are no extant studies, however, that have statistically examined the influence of culturally mediated illness attributions on these variations.


METHODS
We conducted an observational study of 123 (45 White; 35 Black; 43 Asian) patients recruited over a two-year period from an Early Intervention Service (EIS) in Birmingham, UK. Sociodemographic factors (age; sex; education; country of birth; religious practice; marital status; living alone), duration of untreated psychosis (DUP), service contacts (general practitioner; emergency services; faith-based; compulsory detention; criminal justice) and illness attributions ("individual;" "natural;" "social;" "supernatural;" "no attribution") were assessed.


RESULTS
Ethnic groups did not differ in DUP (p = 0.86). Asian patients were more likely to report supernatural illness attributions in comparison to White (Odds Ratio: 4.02; 95 % Confidence Intervals: 1.52, 10.62) and Black (OR: 3.48; 95 % CI: 1.25, 9.67) patients. In logistic regressions controlling for confounders and illness attributions, Black (OR: 14.00; 95 % CI: 1.30, 151.11) and Asian (OR: 13.29; 95 % CI: 1.26, 140.47) patients were more likely to consult faith-based institutions than White patients. Black patients were more likely to be compulsorily detained than White patients (OR: 4.56; 95 % CI: 1.40, 14.85).


CONCLUSION
Illness attributions and sociodemographic confounders do not fully explain the ethnic tendency to seek out faith-based institutions. While Asian and Black patients are more likely to seek help from faith-based organisations, this does not appear to lead to a delay in contact with mental health services.