Miracle-dz/UniFAR-FTUs huggingface dataset:
Solar and Temporal Effects on Escherichia coli Concentration at a Lake Michigan Swimming Beach

ABSTRACT Studies on solar inactivation of Escherichia coli in freshwater and in situ have been limited. At 63rd St. Beach, Chicago, Ill. , factors influencing the daily periodicity of culturable E. coli, particularly insolation, were examined. Water samples for E. coli analysis were collected twice daily between April and September 2000 three times a week along five transects in two depths of water. Hydrometeorological conditions were continuously logged: UV radiation, total insolation, wind speed and direction, wave height, and relative lake level. On 10 days, transects were sampled hourly from 0700 to 1500 h. The effect of sunlight on E. coli inactivation was evaluated with dark and transparent in situ mesocosms and ambient lake water. For the study, the number of E. coli samples collected (n) was 2,676. During sunny days, E. coli counts decreased exponentially with day length and exposure to insolation, but on cloudy days, E. coli inactivation was diminished; the E. coli decay rate was strongly influenced by initial concentration. In situ experiments confirmed that insolation primarily inactivated E. coli; UV radiation only marginally affected E. coli concentration. The relationship between insolation and E. coli density is complicated by relative lake level, wave height, and turbidity, all of which are often products of wind vector. Continuous importation and nighttime replenishment of E. coli were evident. These findings (i) suggest that solar inactivation is an important mechanism for natural reduction of indicator bacteria in large freshwater bodies and (ii) have implications for management strategies of nontidal waters and the use of E. coli as an indicator organism.
A stationary-phase gene in Saccharomyces cerevisiae is a member of a novel, highly conserved gene family

The regulation of cellular growth and proliferation in response to environmental cues is critical for development and the maintenance of viability in all organisms. In unicellular organisms, such as the budding yeast Saccharomyces cerevisiae, growth and proliferation are regulated by nutrient availability. We have described changes in the pattern of protein synthesis during the growth of S. cerevisiae cells to stationary phase (E. K. Fuge, E. L. Braun, and M. Werner-Washburne, J. Bacteriol. 176:5802-5813, 1994) and noted a protein, which we designated Snz1p (p35), that shows increased synthesis after entry into stationary phase. We report here the identification of the SNZ1 gene, which encodes this protein. We detected increased SNZ1 mRNA accumulation almost 2 days after glucose exhaustion, significantly later than that of mRNAs encoded by other postexponential genes. SNZ1-related sequences were detected in phylogenetically diverse organisms by sequence comparisons and low-stringency hybridization. Multiple SNZ1-related sequences were detected in some organisms, including S. cerevisiae. Snz1p was found to be among the most evolutionarily conserved proteins currently identified, indicating that we have identified a novel, highly conserved protein involved in growth arrest in S. cerevisiae. The broad phylogenetic distribution, the regulation of the SNZ1 mRNA and protein in S. cerevisiae, and identification of a Snz protein modified during sporulation in the gram-positive bacterium Bacillus subtilis support the hypothesis that Snz proteins are part of an ancient response that occurs during nutrient limitation and growth arrest.
MEASUREMENTS AT THE NSLS X-RAY RING

Work has been ongoing at the NSLS to improve the orbit stability of the X-Ray Ring by accounting for the thermal motion of the vacuum chamber, which supports the electron beam position monitors (BPMs). In-situ contact measurements of the vacuum chamber motion have been carried out using support stands that have been designed and extensively tested to reduce errors associated with thermal changes in the stands themselves. Using this chamber motion as a correction to the orbit motion measured by the BPMs, the precise location of the radiation beam can be predicted. These predictions are compared with actual radiation beam measurements on the experimental floor, and with predictions based solely on BPM measurements of the electron beam position. This paper reviews this work including stand design and performance, chamber motion measurements, predictions based on these data, and results.
The Karlsruhe Metabolomics and Nutrition (KarMeN) Study: Protocol and Methods of a Cross-Sectional Study to Characterize the Metabolome of Healthy Men and Women

Background The human metabolome is influenced by various intrinsic and extrinsic factors. A precondition to identify such biomarkers is the comprehensive understanding of the composition and variability of the metabolome of healthy humans. Sample handling aspects have an important impact on the composition of the metabolome; therefore, it is crucial for any metabolomics study to standardize protocols on sample collection, preanalytical sample handling, storage, and analytics to keep the nonbiological variability as low as possible. Objective The main objective of the KarMeN study is to analyze the human metabolome in blood and urine by targeted and untargeted metabolite profiling (gas chromatography-mass spectrometry [GC-MS], GC×GC-MS, liquid chromatography-mass spectrometry [LC-MS/MS], and1H nuclear magnetic resonance [NMR] spectroscopy) and to determine the impact of sex, age, body composition, diet, and physical activity on metabolite profiles of healthy women and men. Here, we report the outline of the study protocol with special regard to all aspects that should be considered in studies applying metabolomics. Methods Healthy men and women, aged 18 years or older, were recruited. In addition to a number of anthropometric (height, weight, body mass index, waist circumference, body composition), clinical (blood pressure, electrocardiogram, blood and urine clinical chemistry) and functional parameters (lung function, arterial stiffness), resting metabolic rate, physical activity, fitness, and dietary intake were assessed, and 24-hour urine, fasting spot urine, and plasma samples were collected. Standard operating procedures were established for all steps of the study design. Using different analytical techniques (LC-MS, GC×GC-MS,1H NMR spectroscopy), metabolite profiles of urine and plasma were determined. Data will be analyzed using univariate and multivariate as well as predictive modeling methods. Results The project was funded in 2011 and enrollment was carried out between March 2012 and July 2013. A total of 301 volunteers were eligible to participate in the study. Metabolite profiling of plasma and urine samples has been completed and data analysis is currently underway. Conclusions We established the KarMeN study applying a broad set of clinical and physiological examinations with a high degree of standardization. Our experimental approach of combining scheduled timing of examinations and sampling with the multiplatform approach (GC×GC-MS, GC-MS, LC-MS/MS, and1H NMR spectroscopy) will enable us to differentiate between current and long-term effects of diet and physical activity on metabolite profiles, while enabling us at the same time to consider confounders such as age and sex in the KarMeN study. Trial Registration German Clinical Trials Register DRKS00004890; https://drks-neu.uniklinik-freiburg.de/drks_web/navigate.do? navigationId=trial.HTML&TRIAL_ID=DRKS00004890 (Archived by WebCite at http://www.webcitation.org/6iyM8dMtx)
The assessment of leaf water content using leaf reflectance ratios in the visible, near‐, and short‐wave‐infrared

The common features of spectral reflectance from vegetation foliage upon leaf dehydration are decreasing water absorption troughs in the near‐infrared (NIR) and short‐wave‐infrared (SWIR). We studied which leaf water index in the NIR and SWIR is most suitable for the assessment of leaf water content and the detection of leaf dehydration from the laboratory standpoint. We also examined the influence of the thickness of leaves upon leaf water indices. All leaf water content indices examined exhibited basic correlations with the relative water content (RWC) of leaves, while the R 1300/R 1450 leaf water index also demonstrated a high signal strength and low variability (R 2>0.94). All examined leaf reflectance ratios could also be correlated with leaf thickness. The thickness of leaves, however, was not independent of leaf RWC but appeared to decrease substantially as a result of leaf dehydration.
Synchronization-based computation through networks of coupled oscillators

The mesoscopic activity of the brain is strongly dynamical, while at the same time exhibits remarkable computational capabilities. In order to examine how these two features coexist, here we show that the patterns of synchronized oscillations displayed by networks of neural mass models, representing cortical columns, can be used as substrates for Boolean-like computations. Our results reveal that the same neural mass network may process different combinations of dynamical inputs as different logical operations or combinations of them. This dynamical feature of the network allows it to process complex inputs in a very sophisticated manner. The results are reproduced experimentally with electronic circuits of coupled Chua oscillators, showing the robustness of this kind of computation to the intrinsic noise and parameter mismatch of the coupled oscillators. We also show that the information-processing capabilities of coupled oscillations go beyond the simple juxtaposition of logic gates.
Belief propagation based decoding of large non-orthogonal STBCs

In this paper, we present a belief propagation (BP) based algorithm for decoding non-orthogonal space-time block codes (STBC) from cyclic division algebras (CDA) having large dimensions. The proposed approach involves message passing on Markov random field (MRF) representation of the STBC MIMO system. Adoption of BP approach to decode non-orthogonal STBCs of large dimensions has not been reported so far. Our simulation results show that the proposed BP-based decoding achieves increasingly closer to SISO AWGN performance for increased number of dimensions. In addition, it also achieves near-capacity turbo coded BER performance; for e.g., with BP decoding of 24 × 24 STBC from CDA using BPSK (i.e., 576 real dimensions) and rate-1/2 turbo code (i.e., 12 bps/Hz spectral efficiency), coded BER performance close to within just about 2.5 dB from the theoretical MIMO capacity is achieved.
A Geometrical Model for DNA Organization in Bacteria

Recent experimental studies have revealed that bacteria, such as C. crescentus, show a remarkable spatial ordering of their chromosome. A strong linear correlation has been found between the position of genes on the chromosomal map and their spatial position in the cellular volume. We show that this correlation can be explained by a purely geometrical model. Namely, self-avoidance of DNA, specific positioning of one or few DNA loci (such as origin or terminus) together with the action of DNA compaction proteins (that organize the chromosome into topological domains) are sufficient to get a linear arrangement of the chromosome along the cell axis. We develop a Monte-Carlo method that allows us to test our model numerically and to analyze the dependence of the spatial ordering on various physiologically relevant parameters. We show that the proposed geometrical ordering mechanism is robust and universal (i.e. does not depend on specific bacterial details). The geometrical mechanism should work in all bacteria that have compacted chromosomes with spatially fixed regions. We use our model to make specific and experimentally testable predictions about the spatial arrangement of the chromosome in mutants of C. crescentus and the growth-stage dependent ordering in E. coli.
The complexity of 2-coloring and strong coloring in uniform hypergraphs of high minimum degree

In this paper we consider the problem of deciding whether a given r-uniform hypergraph H with minimum vertex degree at least c\binom|V(H)|-1r-1, or minimum degree of a pair of vertices at least c\binom|V(H)|-2r-2, has a vertex 2-coloring. Motivated by an old result of Edwards for graphs, we obtain first optimal dichotomy results for 2-colorings of r-uniform hypergraphs. For each problem, for every r≥q 3 we determine a threshold value depending on r such that the problem is NP-complete for c below the threshold, while for c strictly above the threshold it is polynomial. We provide an algorithm constructing the coloring with time complexity O(n^\lfloor 4/e\rfloor+2\log n) with some e>0. This algorithm becomes more efficient in the case of r=3,4,5 due to known Turan numbers of the triangle and the Fano plane. In addition, we determine the computational complexity of strong k-coloring of 3-uniform hypergraphs H with minimum vertex degree at least c\binom|V(H)|-12, for some c, leaving a gap for k≥q 5 which vanishes as k→ ∞.
Sentimatrix – Multilingual Sentiment Analysis Service

This paper describes the preliminary results of a system for extracting sentiments opinioned with regard with named entities. It also combines rule-based classification, statistics and machine learning in a new method. The accuracy and speed of extraction and classification are crucial. The service oriented architecture permits the end-user to work with a flexible interface in order to produce applications that range from aggregating consumer feedback on commercial products to measuring public opinion on political issues from blog and forums. The experiment has two versions available for testing, one with concrete extraction results and sentiment calculus and the other with internal metrics validation results.
Bupropion: a systematic review and meta-analysis of effectiveness as an antidepressant

Bupropion has been used as an antidepressant for over 20 years, though its licence for such use varies and it is typically a third- or fourth-line agent. It has a unique pharmacology, inhibiting the reuptake of noradrenaline and dopamine, potentially providing pharmacological augmentation to more common antidepressants such as selective serotonergic reuptake inhibitors (SSRIs). This systematic review and meta-analysis identified 51 studies, dividing into four categories: bupropion as a sole antidepressant, bupropion coprescribed with another antidepressant, bupropion in ‘other’ populations (e.g. bipolar depression, elderly populations) and primary evaluation of side effects. Methodologically more robust trials support the superiority of bupropion over placebo, and most head-to-head antidepressant trials showed an equivalent effectiveness, though some of these are hindered by a lack of a placebo arm. Most work on the coprescribing of bupropion with another antidepressant supports an additional effect, though many are open-label trials. Several large multi-medication trials, most notably STAR*D, also support a therapeutic role for bupropion; in general, it demonstrated similar effectiveness to other medications, though this literature highlights the generally low response rates in refractory cohorts. Effectiveness has been shown in ‘other’ populations, though there is an overall dearth of research. Bupropion is generally well tolerated, it has very low rates of sexual dysfunction, and is more likely to cause weight loss than gain. Our findings support the use of bupropion as a sole or coprescribed antidepressant, particularly if weight gain or sexual dysfunction are, or are likely to be, significant problems. However there are notable gaps in the literature, including less information on treatment naïve and first presentation depression, particularly when one considers the ever-reducing rates of response in more refractory illness. There are some data to support bupropion targeting specific symptoms, but insufficient information to reliably inform such prescribing, and it remains uncertain whether bupropion pharmacodynamically truly augments other drugs.
Fusion of Depth and Color Images for Dense Simultaneous Localization and Mapping

This paper presents a system for performing dense mapping of surface geometry and texture properties. Co-registered depth and grayscale images are incrementally fused into a global map in real-time as they are collected. The resulting dense map can be rendered into a virtual depth and grayscale image from any arbitrary pose. Comparison of the rendered and observed images provides a direct means of computing the sensor pose relative to the map allowing new data to be fused into the model. This frame-to-map tracking scheme, as opposed to frame-toframe tracking, improves system accuracy and robustness. Additionally, the use of both surface geometry and color texture better constrains the pose solution and reduces the risk of tracking failures. This paper describes an implementation of the proposed algorithm and provides experimental results.
Software-defined radio based measurement platform for wireless networks

End-to-end latency is critical to many distributed applications and services that are based on computer networks. There has been a dramatic push to adopt wireless networking technologies and protocols (such as WiFi, ZigBee, WirelessHART, Bluetooth, ISA100.11a, etc.) into time-critical applications. Examples of such applications include industrial automation, telecommunications, power utility, and financial services. While performance measurement of wired networks has been extensively studied, measuring and quantifying the performance of wireless networks face new challenges and demand different approaches and techniques. In this paper, we describe our work in progress of designing a measurement platform based on the technologies of software-defined radio (SDR) and IEEE 1588 Precision Time Protocol (PTP) for evaluating the performance of wireless networks.
The geography of Bangladeshi migration to Rome.

"With reference to the Bangladeshi community in Rome, this paper provides some answers to three key geographical questions: what is the migrants' regional pattern of origin in their home country; what are the mechanisms and routes of their migration to Italy; how are they spatially distributed in Rome? Chain migration links specific origins in Bangladesh with spatial clusters and economic activities in Rome; the key here is the role of Bangladeshi community leaders in Rome who act both as migration sponsors and entrepreneurs. "
Identiﬁcation and Characterization of Two Novel Staphylococcal Enterotoxins, Types S and T (cid:1)

In addition to two known staphylococcal enterotoxin-like genes ( selj and selr ), two novel genes coding for two superantigens, staphylococcal enterotoxins S and T (SES and SET), were identiﬁed in plasmid pF5, which is harbored by food poisoning-related Staphylococcus aureus strain Fukuoka 5. This strain was implicated in a food poisoning incident in Fukuoka City, Japan, in 1997. Recombinant SES (rSES) speciﬁcally stimulated human T cells in a T-cell receptor V (cid:1) 9- and V (cid:1) 16-speciﬁc manner in the presence of major histocompatibility complex (MHC) class II (cid:2) antigen-presenting cells (APC). rSET also stimulated T cells in the presence of MHC class II (cid:2) APC, although its V (cid:1) skewing was not found in reactive T cells. Subsequently, we examined the emetic activity of SES and SET. We also studied SElR to determine emetic activity in primates. This toxin was identiﬁed in previous studies but was not examined in terms of possession of emetic activity for primates. rSES induced emetic reactions in two of four monkeys at a dose of 100 (cid:3) g/kg withi n 5 h ofintragastric administration. In one monkey, rSET induced a delayed reaction (24 h postadministration) at a dose of 100 (cid:3) g/kg, and in the other one, the reaction occurred 5 days postadministration. rSElR induced a reaction in two of six animals withi n 5 h at 100 (cid:3) g/kg. On this basis, we speculate that the causative toxins of vomiting in the Fukuoka case are SES and SER. Additionally, SES, SER, and SET also induced emesis in house musk shrews as in the monkeys.
Recent Development in Ultrasonic Guided Waves for Aircraft and Composite Materials

Emphasis in the paper is placed on describing guided wave successes and challenges for applications in aircraft and composite materials inspection. Guided wave imaging methods discussed includes line of sight, tomography, guided wave C-scan, phased array, and ultrasonic vibration methods. Applications outlined encircles lap splice, bonded repair patch, fuselage corrosion, water loaded structures, delamination, and ice detection and de-icing of various structures.
Annotation Guidelines for the Chinese Proposition Bank

The purpose of the Chinese PropBank (CPB) project is to add a layer of annotation to the hand-parsed sentences in the Chinese Treebank (CTB) (Xue et al., 2005). This layer of annotation assigns predicatespecific argument labels to the constituents in a parse tree. The arguments of each predicate in the sentence, which are limited to verbs and their nominalizations in the work we report here, receive an argument label in the form of ArgN, where N is an integer between 0 and 5. These numbered arguments represent core arguments that are defined in relation to the predicate, which is labeled as Rel. Each core argument plays a unique role with regard to the predicate and generally the total number of core arguments for each predicate does not exceed 6. The core arguments annotated for the verb N (”investigate”) in Example (1) are the NPs (”the police”) and (”accident”) I(”cause”), which are labeled as Arg0 and Arg1 respectively. The semantic role labels added to the parse tree are in bold.
Colorectal cancer screening amongst first degree relatives of colon cancer cases in Jordan.

OBJECTIVES Early detection and screening for colorectal cancer is important among first degree relatives (FDR) of colon cancer cases. METHODS Our target population comprised all such FDR, above 40 years of age, registered during the years 2003-2007, Jordan. Detailed information about cancer cases was collected from Jordan Cancer Registry. The screening study was conducted through two stages, where all FDR were examined at their homes for any suggestive related symptoms of colorectal cancer, then those who were suspected to have cancer were referred to hospital for confirmatory colonoscopy. RESULTS First degree relatives amounted to 3,574 subjects, 153 (4.3%) were complaining of signs and/or symptoms suggestive of CRC. Of them 58 (37.9%) did not accept colonoscopy. The confirmation colonoscopy results for the remaining 95 (62.1%) indicated two confirmed CRC cases. Seventy three percent of the suspected cases complained mainly from change in bowel habit and about one fifth felt cramping. CONCLUSION This study raised the question of cost effectiveness and cost benefits of running a nationwide screening program for such cancer in a developing country. On the other hand it highlights the importance of early detection activities in Jordan as it was the first study to be conducted among a community dwelling high risk population in the country.