Miracle-dz/UniFAR-FTUs huggingface dataset:
Accuracy, Reproducibility, and Interpretation of Fatty Acid Methyl Ester Profiles of Model Bacterial Communities

We determined the accuracy and reproducibility of whole-community fatty acid methyl ester (FAME) analysis with two model bacterial communities differing in composition by using the Microbial ID, Inc. (MIDI), system. The biomass, taxonomic structure, and expected MIDI-FAME profiles under a variety of environmental conditions were known for these model communities a priori. Not all members of each community could be detected in the composite profile because of lack of fatty acid “signatures” in some isolates or because of variations (approximately fivefold) in fatty acid yield across taxa. MIDI-FAME profiles of replicate subsamples of a given community were similar in terms of fatty acid yield per unit of community dry weight and relative proportions of specific fatty acids. Principal-components analysis (PCA) of MIDI-FAME profiles resulted in a clear separation of the two different communities and a clustering of replicates of each community from two separate experiments on the first PCA axis. The first PCA axis accounted for 57.1% of the variance in the data and was correlated with fatty acids that varied significantly between communities and reflected the underlying community taxonomic structure. On the basis of our data, community fatty acid profiles can be used to assess the relative similarities and differences of microbial communities that differ in taxonomic composition. However, detailed interpretation of community fatty acid profiles in terms of biomass or community taxonomic composition must be viewed with caution until our knowledge of the quantitative and qualitative distribution of fatty acids over a wide variety of taxa and the effects of growth conditions on fatty acid profiles is more extensive.
Genetic Studies of Pangwalas, Transhumant and Settled Gaddis: Age Changes in Biological Variables among Pangwalas of Pangi Tehsil, Chamba District, Himachal Pradesh

Abstract In the present paper 37 biological variables (26 anthropometric; 2 physiological and 8 physical fitness tests) have been reported among Pangwala boys with their age ranging from 8+ to 18+ years. The anthropometric and physiological variables show gradual rise from 8+ to 18+ year generally, where as for physical fitnesss tests, in general, a uniform trend of growth is not observed. When compared for anthropometric variables with Transhumant and Settled Gaddis, Pangwalas are showing similar results, in general, whereas for physiological and physical fitness tests variables variation has been observed with Gaduliya Lohars, which may be attributed to their different physical, biological and social environment.
Neural Text Generation from Structured Data with Application to the Biography Domain

This paper introduces a neural model for concept-to-text generation that scales to large, rich domains. We experiment with a new dataset of biographies from Wikipedia that is an order of magnitude larger than existing resources with over 700k samples. The dataset is also vastly more diverse with a 400k vocabulary, compared to a few hundred words for Weathergov or Robocup. Our model builds upon recent work on conditional neural language model for text generation. To deal with the large vocabulary, we extend these models to mix a fixed vocabulary with copy actions that transfer sample-specific words from the input database to the generated output sentence. Our neural model significantly out-performs a classical Kneser-Ney language model adapted to this task by nearly 15 BLEU.
Contributory Factors to Diabetes Dietary Regimen Non Adherence in Adults with Diabetes

A cross sectional survey design was used to collect data from 370 diabetic patients. Two instruments were used in obtaining data; in-depth interview guide and researchers’ developed questionnaire. Fisher's exact test was used to investigate association between the identified factors and nonadherence. Factors identified were: socio-demographic factors such as: gender, age, marital status, educational level and occupation; psychosocial obstacles such as: non-affordability of prescribed diet, frustration due to the restriction, limited spousal support, feelings of deprivation, feeling that temptation is inevitable, difficulty in adhering in social gatherings and difficulty in revealing to host that one is diabetic; health care providers obstacles were: poor attitude of health workers, irregular diabetes education in clinics , limited number of nutrition education sessions/ inability of the patients to estimate the desired quantity of food, no reminder post cards or phone calls about upcoming patient appointments and delayed start of appointment / time wasting in clinics. Keywords—Behavior change, diabetes mellitus, dietary management, diet adherence.
Volcano Seismicity in Alaska

I examine the many facets of volcano seismicity in Alaska: from the short-lived eruption seismicity that is limited to only the few weeks during which a volcano is active, to the seismicity that occurs in the months following an eruption, and finally to the longterm volcano seismicity that occurs in the years in which volcanoes are dormant. I use the rich seismic dataset that was recorded during the 2009 eruption of Redoubt Volcano to examine eruptive volcano seismicity. I show that the progression of magma through the conduit system at Redoubt could be readily tracked by the seismicity. Many of my interpretations benefited greatly from the numerous other datasets collected during the eruption. Rarely was there volcanic activity that did not manifest itself in some way seismically, however, resulting in a remarkably complete chronology within the seismic record of the 2009 eruption. I also use the Redoubt seismic dataset to study post-eruptive seismicity. During the year following the eruption there were a number of unexplained bursts of shallow seismicity that did not culminate in eruptive activity despite closely mirroring seismic signals that had preceded explosions less than a year prior. I show that these episodes of shallow seismicity were in fact related to volcanic processes much deeper in the volcanic edifice by demonstrating that earthquakes that were related to magmatic activity during the eruption were also present during the renewed shallow unrest. These results show that magmatic processes can continue for many months after eruptions end, suggesting that volcanoes can stay active for much longer than previously thought. In the final chapter I characterize volcanic earthquakes on a much broader scale by analyzing a decade of continuous seismic data across 46 volcanoes in the Aleutian arc to search for regional-scale trends in volcano seismicity. I find that volcanic earthquakes below 20 km depth are much more common in the central region of the arc than they are in the eastern and western regions. I tie these observations to trends in magma
Mitochondrial Epigenetic Changes Link to Increased Diabetes Risk and Early-Stage Prediabetes Indicator

Type 2 diabetes (T2D) is characterized by mitochondrial derangement and oxidative stress. With no known cure for T2D, it is critical to identify mitochondrial biomarkers for early diagnosis of prediabetes and disease prevention. Here we examined 87 participants on the diagnosis power of fasting glucose (FG) and hemoglobin A1c levels and investigated their interactions with mitochondrial DNA methylation. FG and A1c led to discordant diagnostic results irrespective of increased body mass index (BMI), underscoring the need of new biomarkers for prediabetes diagnosis. Mitochondrial DNA methylation levels were not correlated with late-stage (impaired FG or A1c) but significantly with early-stage (impaired insulin sensitivity) events. Quartiles of BMI suggested that mitochondrial DNA methylation increased drastically from Q1 (20 < BMI < 24.9, lean) to Q2 (30 < BMI < 34.9, obese), but marginally from Q2 to Q3 (35 < BMI < 39.9, severely obese) and from Q3 to Q4 (BMI > 40, morbidly obese). A significant change was also observed from Q1 to Q2 in HOMA insulin sensitivity but not in A1c or FG. Thus, mitochondrial epigenetic changes link to increased diabetes risk and the indicator of early-stage prediabetes. Further larger-scale studies to examine the potential of mitochondrial epigenetic marker in prediabetes diagnosis will be of critical importance for T2D prevention.
Evaluation of Group Cognitive Behavioral Therapy for Adults With ADHD

Objective: A brief cognitive behavioral therapy (CBT) group intervention was designed to treat comorbid anxiety, depression, and low self-esteem and self-efficacy in adults with ADHD. It was hypothesised that participants would gain knowledge about ADHD, experience a reduction in comorbid symptoms, and benefit from the supportive aspect of group treatment. Method: Participants in the study formed a CBT treatment group that attended six workshops and a waiting list control group. The intervention was evaluated with measures assessing knowledge about ADHD, psychological symptoms, and support received. The groups were compared using repeated measures ANOVAs. Results: The CBT group had significantly greater improvement on measures of knowledge about ADHD, self-efficacy, and self-esteem than the control group. Participants' evaluations of the sessions suggested that sharing personal experiences with other adults with ADHD was an important aspect of the intervention. Conclusion: Brief CBT group treatments may be an acceptable and cost-effective intervention for adults with ADHD. (J. of Att. Dis. 2009; 12(5) 434-441)
Sulfate-Reducing Bacteria in Tubes Constructed by the Marine Infaunal Polychaete Diopatra cuprea

ABSTRACT Marine infaunal burrows and tubes greatly enhance solute transport between sediments and the overlying water column and are sites of elevated microbial activity. Biotic and abiotic controls of the compositions and activities of burrow and tube microbial communities are poorly understood. The microbial communities in tubes of the marine infaunal polychaete Diopatria cuprea collected from two different sediment habitats were examined. The bacterial communities in the tubes from a sandy sediment differed from those in the tubes from a muddy sediment. The difference in community structure also extended to the sulfate-reducing bacterial (SRB) assemblage, although it was not as pronounced for this functional group of species. PCR-amplified 16S rRNA gene sequences recovered from Diopatra tube SRB by clonal library construction and screening were all related to the family Desulfobacteriaceae. This finding was supported by phospholipid fatty acid analysis and by hybridization of 16S rRNA probes specific for members of the genera Desulfosarcina, Desulfobacter, Desulfobacterium, Desulfobotulus, Desulfococcus, and Desulfovibrio and some members of the genera Desulfomonas, Desulfuromonas, and Desulfomicrobium with 16S rRNA gene sequences resolved by denaturing gradient gel electrophoresis. Two of six SRB clones from the clone library were not detected in tubes from the sandy sediment. The habitat in which the D. cuprea tubes were constructed had a strong influence on the tube bacterial community as a whole, as well as on the SRB assemblage.
Effect of Stacked Insecticidal Cry Proteins from Maize Pollen on Nurse Bees (Apis mellifera carnica) and Their Gut Bacteria

Honey bee pollination is a key ecosystem service to nature and agriculture. However, biosafety research on genetically modified crops rarely considers effects on nurse bees from intact colonies, even though they receive and primarily process the largest amount of pollen. The objective of this study was to analyze the response of nurse bees and their gut bacteria to pollen from Bt maize expressing three different insecticidal Cry proteins (Cry1A.105, Cry2Ab2, and Cry3Bb1). Naturally Cry proteins are produced by bacteria (Bacillus thuringiensis). Colonies of Apis mellifera carnica were kept during anthesis in flight cages on field plots with the Bt maize, two different conventionally bred maize varieties, and without cages, 1-km outside of the experimental maize field to allow ad libitum foraging to mixed pollen sources. During their 10-days life span, the consumption of Bt maize pollen had no effect on their survival rate, body weight and rates of pollen digestion compared to the conventional maize varieties. As indicated by ELISA-quantification of Cry1A.105 and Cry3Bb1, more than 98% of the recombinant proteins were degraded. Bacterial population sizes in the gut were not affected by the genetic modification. Bt-maize, conventional varieties and mixed pollen sources selected for significantly different bacterial communities which were, however, composed of the same dominant members, including Proteobacteria in the midgut and Lactobacillus sp. and Bifidobacterium sp. in the hindgut. Surprisingly, Cry proteins from natural sources, most likely B. thuringiensis, were detected in bees with no exposure to Bt maize. The natural occurrence of Cry proteins and the lack of detectable effects on nurse bees and their gut bacteria give no indication for harmful effects of this Bt maize on nurse honey bees.
LCIS: a boundary hierarchy for detail-preserving contrast reduction

High contrast scenes are difficult to depict on low contrast displays without loss of important fine details and textures. Skilled artists preserve these details by drawing scene contents in coarseto-fine order using a hierarchy of scene boundaries and shadings. We build a similar hierarchy using multiple instances of a new low curvature image simplifier (LCIS), a partial differential equation inspired by anisotropic diffusion. Each LCIS reduces the scene to many smooth regions that are bounded by sharp gradient discontinuities, and a single parameter K chosen for each LCIS controls region size and boundary complexity. With a few chosen K values (K1 > K2 > K3:::) LCIS makes a set of progressively simpler images, and image differences form a hierarchy of increasingly important details, boundaries and large features. We construct a high detail, low contrast display image from this hierarchy by compressing only the large features, then adding back all small details. Unlike linear filter hierarchies such as wavelets, filter banks, or image pyramids, LCIS hierarchies do not smooth across scene boundaries, avoiding “halo” artifacts common to previous contrast reducing methods and some tone reproduction operators. We demonstrate LCIS effectiveness on several example images. CR Descriptors: I.3. 3 [Computer Graphics]: Picture/image generation Display algorithms; I.4. 1 [Image Processing and Computer Vision]: Enhancement -Digitization and Image Capture
Parameter estimation in total variation blind deconvolution

In this paper we present a methodology for parameter estimation in total variation (TV) blind deconvolution. By formulating the problem in a Bayesian framework, the unknown image, blur and the model parameters are simultaneously estimated. The resulting algorithms provide approximations to the posterior distributions of the unknowns by utilizing variational distribution approximations. We show that some of the current approaches towards TV-based blind deconvolution are special cases of our formulation. Experimental results are provided to demonstrate the performance of the algorithms.
Simultaneous Compensation of Polarization Mode Dispersion and Chromatic Dispersion Using Electronic Signal Processing

In this paper, we study the performance of 10.7-Gb/s nonreturn-to-zero (NRZ) and return-to-zero (RZ) on-off keying signals in the joint presence of first-order polarization mode dispersion (PMD) and chromatic dispersion (CD) based on optical signal-to-noise ratio penalty measurements. Our investigations show that the tolerance of RZ to first-order PMD is severely reduced by the presence of typical values of residual CD. Three different receiver strategies are studied: 1. unequalized threshold detection; 2. combined feed-forward and decision-feedback equalization; and 3. maximum-likelihood sequence estimation (MLSE). In all three cases, the presence of CD eliminates the advantage of RZ over NRZ in terms of PMD tolerance. For NRZ, we find that the MLSE improves the tolerance to first-order PMD by 60%-70%, even in the presence of residual CD.
Approximation algorithms for precedence-constrained scheduling problems on parallel machines that run at different speeds

We present new approximation algorithms for the problem of scheduling precedence-constrained jobs on parallel machines that are uniformly related. That is, there are n jobs and m machines; each job j requires p{sub j} units of processing, and is to be processed on one machine without interruption; if it is assigned to machine i, which runs at a given speed s{sub i}, it takes p{sub j}/s{sub i} time units. There also is a partial order {prec} on the jobs, where j {prec} k implies that job k may not start processing until job j has been completed. We shall consider two objective functions: C{sub max} = max{sub j} C{sub j}, where C{sub j} denotes the completion time of job j, and {Sigma}{sub j} {omega}{sub j}C{sub j}, where w{sub j} is a weight that is given for each job j. For the first objective, the best previously known result is an O({radical})m-approximation algorithm, which was shown by Jaffe more than 15 years ago. We shall give an O(log m)- approximation algorithm. We shall also show how to extend this result to obtain an O(log m)-approximation algorithm for the second objective, albeit with a somewhat larger constant. These results also extend tomore » settings in which each job j has a release date r{sub j} before which the job may not begin processing. In addition, we obtain stronger performance guarantees if there are a limited number of distinct speeds. Our results are based on a new linear programming-based technique for estimating the speed at which each job should be run, and a variant of the list scheduling algorithm of Graham that can exploit this additional information. « less
C11orf83, a Mitochondrial Cardiolipin-Binding Protein Involved in bc1 Complex Assembly and Supercomplex Stabilization

ABSTRACT Mammalian mitochondria may contain up to 1,500 different proteins, and many of them have neither been confidently identified nor characterized. In this study, we demonstrated that C11orf83, which was lacking experimental characterization, is a mitochondrial inner membrane protein facing the intermembrane space. This protein is specifically associated with the bc1 complex of the electron transport chain and involved in the early stages of its assembly by stabilizing the bc1 core complex. C11orf83 displays some overlapping functions with Cbp4p, a yeast bc1 complex assembly factor. Therefore, we suggest that C11orf83, now called UQCC3, is the functional human equivalent of Cbp4p. In addition, C11orf83 depletion in HeLa cells caused abnormal crista morphology, higher sensitivity to apoptosis, a decreased ATP level due to impaired respiration and subtle, but significant, changes in cardiolipin composition. We showed that C11orf83 binds to cardiolipin by its α-helices 2 and 3 and is involved in the stabilization of bc1 complex-containing supercomplexes, especially the III2/IV supercomplex. We also demonstrated that the OMA1 metalloprotease cleaves C11orf83 in response to mitochondrial depolarization, suggesting a role in the selection of cells with damaged mitochondria for their subsequent elimination by apoptosis, as previously described for OPA1.
Using a priori Information for Regularization in Breast Microwave Image Reconstruction

Regularization methods are used in microwave image reconstruction problems, which are ill-posed. Traditional regularization methods are usually problem-independent and do not take advantage of a priori information specific to any particular imaging application. In this paper, a novel problem-dependent regularization approach is introduced for the application of breast imaging. A real genetic algorithm (RGA) minimizes a cost function that is the error between the recorded and the simulated data. At each iteration of the RGA, a priori information about the shape of the breast profiles is used by a neural network classifier to reject the solutions that cannot be a map of the dielectric properties of a breast profile. The algorithm was tested against four realistic numerical breast phantoms including a mostly fatty, a scattered fibroglandular, a heterogeneously dense, and a very dense sample. The tests were also repeated where a 4 mm × 4 mm tumor was inserted in the fibroglandular tissue in each of the four breast types. The results show the effectiveness of the proposed approach, which to the best of our knowledge has the highest resolution amongst the evolutionary algorithms used for the inversion of realistic numerical breast phantoms.
The Effects of Low-Dose 0.5-mg Melatonin on the Free-Running Circadian Rhythms of Blind Subjects

Exogenous melatonin (0.5-10 mg) has been shown to entrain the free-running circadian rhythms of some blind subjects. The aim of this study was to assess further the entraining effects of a daily dose of 0.5 mg melatonin on the cortisol rhythm and its acute effects on subjective sleep in blind subjects with free-running 6-sulphatoxymelatonin (aMT6s) rhythms (circadian period [τ] 24.23-24.95 h). Ten subjects (9 males) were studied, aged 32 to 65 years, with no conscious light perception (NPL). In a placebo-controlled, single-blind design, subjects received 0.5 mg melatonin or placebo p.o. daily at 2100 h (treatment duration 26-81 days depending on individuals' circadian period). Subjective sleep was assessed from daily sleep and nap diaries. Urinary cortisol and aMT6s were assessed for 24 to 48 h weekly and measured by radioimmunoassay. Seven subjects exhibited an entrained or shortened cortisol period during melatonin treatment. Of these, 4 subjects entrained with a period indistinguishable from 24 h, 2 subjects continued to run for up to 25 days during melatonin treatment before their cortisol rhythm became entrained, and 1 subject appeared to exhibit a shortened cortisol period throughout melatonin treatment. The subjects who entrained within 7 days did so when melatonin treatment commenced in the phase advance portion of the melatonin PRC (CT6-18). When melatonin treatment ceased, cortisol and aMT6s rhythms free ran at a similar period to before treatment. Three subjects failed to entrain with initial melatonin treatment commencing in the phase delay portion of the PRC. During melatonin treatment, there was a of free significant increase in nighttime sleep duration and a reduction in the number and duration of daytime naps. The positive effect of melatonin on sleep may be partly due to its acute soporific properties. The findings demonstrate that a daily dose of 0.5 mg melatonin is effective at entraining the free-running circa-dian systems in most of the blind subjects studied, and that circadian time (CT) of administration Optimal melatonin may be important entrains to melatonin treatment. 24-h sleep disorder should p.o. in determining whether a subject disorder the sleep-wake cycle) in addition to improving sleep acutely. correct treatment with melatonin for the underlying circadian this (to non-entrain