Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling the Adenoma and Serrated Pathway to Colorectal CAncer (ASCCA)

Several colorectal cancer (CRC) screening models have been developed describing the progression of adenomas to CRC. Currently, there is increasing evidence that serrated lesions can also develop into CRC. It is not clear whether screening tests have the same test characteristics for serrated lesions as for adenomas, but lower sensitivities have been suggested. Models that ignore this type of colorectal lesions may provide overly optimistic predictions of the screen‐induced reduction in CRC incidence. To address this issue, we have developed the Adenoma and Serrated pathway to Colorectal CAncer (ASCCA) model that includes the adenoma‐carcinoma pathway and the serrated pathway to CRC as well as characteristics of colorectal lesions. The model structure and the calibration procedure are described in detail. Calibration resulted in 19 parameter sets for the adenoma‐carcinoma pathway and 13 for the serrated pathway that match the age‐ and sex‐specific adenoma and serrated lesion prevalence in the COlonoscopy versus COlonography Screening (COCOS) trial, Dutch CRC incidence and mortality rates, and a number of other intermediate outcomes concerning characteristics of colorectal lesions. As an example, we simulated outcomes for a biennial fecal immunochemical test screening program and a hypothetical one‐time colonoscopy screening program. Inclusion of the serrated pathway influenced the predicted effectiveness of screening when serrated lesions are associated with lower screening test sensitivity or when they are not removed. To our knowledge, this is the first model that explicitly includes the serrated pathway and characteristics of colorectal lesions. It is suitable for the evaluation of the (cost)effectiveness of potential screening strategies for CRC.
Metabolomic Analysis of Diet-Induced Type 2 Diabetes Using UPLC/MS Integrated with Pattern Recognition Approach

Metabolomics represents an emerging discipline concerned with comprehensive assessment of small molecule endogenous metabolites in biological systems and provides a powerful approach insight into the mechanisms of diseases. Type 2 diabetes (T2D), called the burden of the 21st century, is growing with an epidemic rate. However, its precise molecular mechanism has not been comprehensively explored. In this study, we applied urinary metabolomics based on the UPLC/MS integrated with pattern recognition approaches to discover differentiating metabolites, to characterize and explore metabolic pathway disruption in an experimental model for high-fat-diet induced T2D. Six differentiating urinary metabolites were found in the negative mode, and two (2-(4-hydroxy-3-methoxy-phenyl) acetaldehyde sulfate, 2-phenylethanol glucuronide) of which were identified involving the key metabolic pathways linked to pentose and glucuronate interconversions, starch, sucrose metabolism and tyrosine metabolism. Our study provides new insight into pathophysiologic mechanisms and may enhance the understanding of T2D pathogenesis.
Zebrafish response to a robotic replica in three dimensions

As zebrafish emerge as a species of choice for the investigation of biological processes, a number of experimental protocols are being developed to study their social behaviour. While live stimuli may elicit varying response in focal subjects owing to idiosyncrasies, tiredness and circadian rhythms, video stimuli suffer from the absence of physical input and rely only on two-dimensional projections. Robotics has been recently proposed as an alternative approach to generate physical, customizable, effective and consistent stimuli for behavioural phenotyping. Here, we contribute to this field of investigation through a novel four-degree-of-freedom robotics-based platform to manoeuvre a biologically inspired three-dimensionally printed replica. The platform enables three-dimensional motions as well as body oscillations to mimic zebrafish locomotion. In a series of experiments, we demonstrate the differential role of the visual stimuli associated with the biologically inspired replica and its three-dimensional motion. Three-dimensional tracking and information-theoretic tools are complemented to quantify the interaction between zebrafish and the robotic stimulus. Live subjects displayed a robust attraction towards the moving replica, and such attraction was lost when controlling for its visual appearance or motion. This effort is expected to aid zebrafish behavioural phenotyping, by offering a novel approach to generate physical stimuli moving in three dimensions.
Emphatic Visual Speech Synthesis

The synthesis of talking heads has been a flourishing research area over the last few years. Since human beings have an uncanny ability to read people's faces, most related applications (e.g., advertising, video-teleconferencing) require absolutely realistic photometric and behavioral synthesis of faces. This paper proposes a person-specific facial synthesis framework that allows high realism and includes a novel way to control visual emphasis (e.g., level of exaggeration of visible articulatory movements of the vocal tract). There are three main contributions: a geodesic interpolation with visual unit selection, a parameterization of visual emphasis, and the design of minimum size corpora. Perceptual tests with human subjects reveal high realism properties, achieving similar perceptual scores as real samples. Furthermore, the visual emphasis level and two communication styles show a statistical interaction relationship.
Mandatory influenza vaccination of health care workers: translating policy to practice.

BACKGROUND Influenza vaccination of health care workers has been recommended since 1984. Multiple strategies to enhance vaccination rates have been suggested, but national rates have remained low. METHODS BJC HealthCare is a large Midwestern health care organization with approximately 26,000 employees. Because organizational vaccination rates remained below target levels, influenza vaccination was made a condition of employment for all employees in 2008. Medical or religious exemptions could be requested. Predetermined medical contraindications include hypersensitivity to eggs, prior hypersensitivity reaction to influenza vaccine, and history of Guillan-Barré syndrome. Medical exemption requests were reviewed by occupational health nurses and their medical directors. Employees who were neither vaccinated nor exempted by 15 December 2008 were not scheduled for work. Employees still not vaccinated or exempt by 15 January 2009 were terminated. RESULTS Overall, 25,561 (98.4%) of 25,980 active employees were vaccinated. Ninety employees (0.3%) received religious exemptions, and 321 (1.2%) received medical exemptions. Eight employees (0.03%) were not vaccinated or exempted. Reasons for medical exemption included allergy to eggs (107 [33%]), prior allergic reaction or allergy to other vaccine component (83 [26%]), history of Guillan-Barré syndrome (15 [5%]), and other (116 [36%]), including 14 because of pregnancy. Many requests reflected misinformation about the vaccine. CONCLUSIONS A mandatory influenza vaccination campaign successfully increased vaccination rates. Fewer employees sought medical or religious exemptions than had signed declination statements during the previous year. A standardized medical exemption request form would simplify the request and review process for employees, their physicians, and occupational health and will be used next year.
Modulation of cardiac L-type Ca2+ current by angiotensin-(1-7): normal versus heart failure

Objective: Recent evidence has shown that, in heart failure (HF), clinically relevant concentrations of angiotensin-(1-7) [Ang-(1-7)] counteracts angiotensin II induced cardiac depression and produces positive inotropic effects in both left ventricle (LV) and myocytes. However, the underlying electrophysiological mechanism is unclear. We investigated the role and mechanism of Ang-(1-7) on LV myocyte L-type calcium current (ICa,L) responses in normal state and in HF. Method: We compared the effect of Ang-(1-7) (10−5 M) on ICa,L responses in isolated LV myocytes obtained from 11 rats with isoproterenol (ISO) induced HF (3 months after 170 mg/kg subcutaneous for 2 days) and from 8 age-matched normal control rats by patch clamp technique. Results: In normal myocytes, compared with baseline, superfusion of Ang-(1-7) caused no significant changes in ICa,L (8.2 ± 0.2 versus 8.0 ± 0.3 pA/pF, p= not significant). In HF myocytes, the baseline ICa,L was significantly reduced (5.3 ± 0.1 versus 8.0 ± 0.3 pA/pF, p < 0.01). Ang-(1-7) produced a 21% increase in ICa,L (6.4±0.1 versus 5.3±0.1 pA/pF, p < 0.01). Pretreatment of HF myocytes with a nitric oxide (NO) synthase inhibitor (L-NAME, 10−5 M) resulted in a significantly greater increase in ICa,L (28%, 8.4 ± 0.1 versus 6.5 ± 0.1 pA/pF, p < 0.01) during Ang-(1-7) superfusion. In contrast, during incubation with the bradykinin (BK) inhibitor HOE 140 (10−6 M), Ang-(1-7) induced increase in ICa,L was significantly decreased. The Ang-(1-7) induced increase in ICa,L was abolished by [D-Ala7]-Ang-(1-7) (A-779, 10−5 M). Conclusions: HF alters the response of ICa,L to Ang-(1-7). In normal myocytes, Ang-(1-7) has no significant effect on ICa,L. However, in HF myocytes, Ang-(1-7) increases ICa,L. These effects are mediated by the Ang-(1-7) Mas receptors and involve activation of NO/BK pathways.
Vertical Distribution of Ammonia-Oxidizing Crenarchaeota and Methanogens in the Epipelagic Waters of Lake Kivu (Rwanda-Democratic Republic of the Congo)

ABSTRACT Four stratified basins in Lake Kivu (Rwanda-Democratic Republic of the Congo) were sampled in March 2007 to investigate the abundance, distribution, and potential biogeochemical role of planktonic archaea. We used fluorescence in situ hybridization with catalyzed-reported deposition microscopic counts (CARD-FISH), denaturing gradient gel electrophoresis (DGGE) fingerprinting, and quantitative PCR (qPCR) of signature genes for ammonia-oxidizing archaea (16S rRNA for marine Crenarchaeota group 1.1a [MCG1] and ammonia monooxygenase subunit A [amoA]). Abundance of archaea ranged from 1 to 4.5% of total DAPI (4′,6-diamidino-2-phenylindole) counts with maximal concentrations at the oxic-anoxic transition zone (∼50-m depth). Phylogenetic analysis of the archaeal planktonic community revealed a higher level of richness of crenarchaeal 16S rRNA gene sequences (21 of the 28 operational taxonomic units [OTUs] identified [75%]) over euryarchaeotal ones (7 OTUs). Sequences affiliated with the kingdom Euryarchaeota were mainly recovered from the anoxic water compartment and mostly grouped into methanogenic lineages (Methanosarcinales and Methanocellales). In turn, crenarchaeal phylotypes were recovered throughout the sampled epipelagic waters (0- to 100-m depth), with clear phylogenetic segregation along the transition from oxic to anoxic water masses. Thus, whereas in the anoxic hypolimnion crenarchaeotal OTUs were mainly assigned to the miscellaneous crenarchaeotic group, the OTUs from the oxic-anoxic transition and above belonged to Crenarchaeota groups 1.1a and 1.1b, two lineages containing most of the ammonia-oxidizing representatives known so far. The concomitant vertical distribution of both nitrite and nitrate maxima and the copy numbers of both MCG1 16S rRNA and amoA genes suggest the potential implication of Crenarchaeota in nitrification processes occurring in the epilimnetic waters of the lake.
Multiple sclerosis in American blacks

In the period 1968 through 1977, multiple sclerosis (MS) was diagnosed in 349 patients at the Henry Ford Hospital. Of these, 312 were accepted in the study and 53 were blacks. In this medical center where the overall population consists of approximately 50% blacks, the MS blacks comprised only 17 % of the total MS population. White and black MS patients did not differ significantly for clinical characteristics of MS or for death rates. The MS black patients were divided in two groups, Northern‐and Southern‐born. The mean age of migration was 11.9 years. Southern‐born blacks lived an average of 20 years in the North before the symptoms of MS began. Northern‐born MS patients had a 5.5 earlier age of onset and the diagnosis was made 9 years sooner when compared with the Southern‐born MS blacks. The Southern‐born MS group more often showed a chronic progressive course wither initially or following a few exacerbations and remissions. These findings suggest that a possible genetic predisposition, as well as a geographically determined exposure to an environmental agent, may be related not only to the risk of developing MS, but in the American blacks may also influence the age of onset, the age of diagnosis, and even the clinical course of MS.
Fluidized bed silicon deposition

The growth of silicon on seed particles from the pyrolysis of silane in a fluidized bed reactor (FBR) was studied. The grown particles were shown to be crystalline and to have a structure which has been interpreted to indicate growth by chemical vapor deposition as well as by the collection (scavenging) of silicon clusters on seed particle surfaces. Scanning electron microscopy was used to study the product morphology.
‘… a metal conducts and a non-metal doesn't’

In a letter to one of the authors, Sir Nevill Mott, then in his tenth decade, highlighted the fact that the statement ‘… a metal conducts, and a non-metal doesn’t’ can be true only at the absolute zero of temperature, T=0 K. But, of course, experimental studies of metals, non-metals and, indeed, the electronic and thermodynamic transition between these canonical states of matter must always occur above T=0 K, and, in many important cases, for temperatures far above the absolute zero. Here, we review the issues—theoretical and experimental—attendant on studies of the metal to non-metal transition in doped semiconductors at temperatures close to absolute zero (T=0.03 K) and fluid chemical elements at temperatures far above absolute zero (T>1000 K). We attempt to illustrate Mott’s insights for delving into such complex phenomena and experimental systems, finding intuitively the dominant features of the science, and developing a coherent picture of the different competing electronic processes. A particular emphasis is placed on the idea of a ‘Mott metal to non-metal transition’ in the nominally metallic chemical elements rubidium, caesium and mercury, and the converse metallization transition in the nominally non-metal elements hydrogen and oxygen. We also review major innovations by D. A. Goldhammer (Goldhammer 1913 Dispersion und absorption des lichtes) and K. F. Herzfeld (Herzfeld 1927 Phys. Rev. 29, 701–705. (doi:10.1103/PhysRev.29.701)) in a pre-quantum theory description of the metal–non-metal transition, which emphasize the pivotal role of atomic properties in dictating the metallic or non-metallic status of the chemical elements of the periodic table under ambient and extreme conditions; a link with Pauling’s ‘metallic orbital’ is also established here.
Single unit responses to skin odorants from conspecifics and heterospecifics in the olfactory bulb of crucian carp Carassius carassius

SUMMARY Injured fish skin leaks alarm substances that induce the fright reaction upon olfactory detection. The skin also contains a multitude of other odorants traditionally related to other behaviors, but to what extent they are detected upon injury is unknown. We have performed single unit recordings in the olfactory bulb (OB) of crucian carp while exposing the olfactory epithelium to skin extracts from conspecifics and three other species of the carp family, common carp, tench and bream. The aims were to investigate whether neural activity may be induced by different types of skin odorants and how well the odorants from injured conspecifics are distinguished from other species. The OB of crucian carp shows a clear chemotopy as units located in different regions respond to either food-related odorants, to pheromones or to alarm odorants respectively. Units in all regions responded to skin extracts, which indicate the detection of odorants usually involved in reproduction and feeding, in addition to the alarm substances. Among OB units responding to only one of the skin extracts, most were sensitive to conspecific skin extract. Furthermore, pair-wise comparisons showed that the discrimination between conspecific skin extract and skin extract from another species was in general better than the discrimination between skin extracts from two heterospecifics. The findings suggest that identification of injured fishes may be based on different groups of odorants and that the crucian carp olfactory system discriminates well between odorants from conspecifics and those from other fish species.
Complexity Analysis vs. Engineering Design in CSP Algorithms: Contravening Conventional Wisdom Again

In this work we compare simple and ‘advanced’ algorithms that have been used to perform various functions in connection with constraint satisfaction problems (CSPs). These include algorithms for arc consistency, singleton arc consistency, arc consistency used with MAC, maxRPC algorithms, and algorithms for simple table reduction with non-binary constraints. In each case tested so far, we find tradeoffs between efficient implementations of basic operations like constraint checking and elaborations that allow a reduction in the number of these basic operations but add bookkeeping expenses. It is argued that such tradeoffs must be given more thorough consideration. This also suggests that there are interesting theoretical problems in this connection that have not yet received the attention they merit. Finally, the possibility that certain psychological biases have affected the analysis of algorithms in this area is considered.
Tweeting Beyond Tahrir: Ideological Diversity and Political Intolerance in Egyptian Twitter Networks

ABSTRACT:Do online social networks affect political tolerance in the highly polarized climate of postcoup Egypt? Taking advantage of the real-time networked structure of Twitter data, the authors find that not only is greater network diversity associated with lower levels of intolerance, but also that longer exposure to a diverse network is linked to less expression of intolerance over time. The authors find that this relationship persists in both elite and non-elite diverse networks. Exploring the mechanisms by which network diversity might affect tolerance, the authors offer suggestive evidence that social norms in online networks may shape individuals’ propensity to publicly express intolerant attitudes. The findings contribute to the political tolerance literature and enrich the ongoing debate over the relationship between online echo chambers and political attitudes and behavior by providing new insights from a repressive authoritarian context.
Lung resection in patients with preoperative FEV1 < 35% predicted.

OBJECTIVES To determine the morbidity, mortality, and feasibility of lung resection in patients with tumors and preoperative FEV1 < 35% predicted. DESIGN Retrospective review. SETTING A 734-bed, tertiary care, academic hospital with a dedicated general thoracic surgery unit performing > 2,000 operations per year. PATIENTS One hundred consecutive patients with discrete lung tumors and with preoperative FEV1 < 35% predicted undergoing lung resection between September 1997 and May 2003. Only operations with curative intent were included. Average preoperative predicted FEV1 was 26%. Sixteen percent of the patients were oxygen dependent prior to the operation. RESULTS Open and thoracoscopic wedge resections, segmentectomies, lobectomies, and combined lung resections with lung volume reduction were performed. Sixty-six of the lesions were malignant, and 57 were primary lung cancers. Only one patient left the operating room with positive margins. There was one in-hospital or 30-day mortality. Thirty-six percent of the patients had one or more complications. Twenty-two percent of the patients had prolonged air leaks requiring a chest tube for > 7 days. One patient left the hospital ventilator dependent, 3 additional patients required intubation > 48 h, and 11 patients were discharged with a new oxygen requirement. There were four pneumonias, one myocardial infarction, and two reoperations for bleeding. Male gender (p = 0.003), preoperative oxygen dependence (p = 0.03), and pack-year history (p = 0.006) were associated with a higher overall incidence of complications, while age, incision, diabetes, coronary artery disease, duration of smoking cessation, amount of lung resected, size of lesion, and preoperative percentage of predicted FEV1 did not correlate with the overall incidence of complications. CONCLUSIONS In a large academic center, minimally invasive surgical techniques, intensive pulmonary care, and advanced anesthetic techniques allow for curative lung tumor resections in patients with very low preoperative FEV1 with a very low mortality and very low incidence of ventilator dependence. Other serious complications such as pneumonia, myocardial infarction, and bleeding are uncommon. An extended hospital stay and a high incidence of prolonged air leak should be expected, especially in patients with preoperative FEV1 < or = 20% predicted.
EssOilDB: a database of essential oils reflecting terpene composition and variability in the plant kingdom

Plant essential oils are complex mixtures of volatile organic compounds, which play indispensable roles in the environment, for the plant itself, as well as for humans. The potential biological information stored in essential oil composition data can provide an insight into the silent language of plants, and the roles of these chemical emissions in defense, communication and pollinator attraction. In order to decipher volatile profile patterns from a global perspective, we have developed the ESSential OIL DataBase (EssOilDB), a continually updated, freely available electronic database designed to provide knowledge resource for plant essential oils, that enables one to address a multitude of queries on volatile profiles of native, invasive, normal or stressed plants, across taxonomic clades, geographical locations and several other biotic and abiotic influences. To our knowledge, EssOilDB is the only database in the public domain providing an opportunity for context based scientific research on volatile patterns in plants. EssOilDB presently contains 123 041 essential oil records spanning a century of published reports on volatile profiles, with data from 92 plant taxonomic families, spread across diverse geographical locations all over the globe. We hope that this huge repository of VOCs will facilitate unraveling of the true significance of volatiles in plants, along with creating potential avenues for industrial applications of essential oils. We also illustrate the use of this database in terpene biology and show how EssOilDB can be used to complement data from computational genomics to gain insights into the diversity and variability of terpenoids in the plant kingdom. EssOilDB would serve as a valuable information resource, for students and researchers in plant biology, in the design and discovery of new odor profiles, as well as for entrepreneurs—the potential for generating consumer specific scents being one of the most attractive and interesting topics in the cosmetic industry. Database URL: http://nipgr.res.in/Essoildb/