Miracle-dz/UniFAR-FTUs huggingface dataset:
Intrinsic Ictal Dynamics at the Seizure Focus: Effects of Secondary Generalization Revealed by Complexity Measures

Summary: Purpose: Partial seizures (PSs) may be self‐limited regional events or propagate further and secondarily generalize. The mechanisms and dynamics of secondarily generalized tonic–clonic seizures (GTCSs) are not well understood. Methods with which to assess the dynamic of those events are also limited.
Cubic surface fitting to image with edges as constraints

Conventional polynomial interpolation methods produce images with blurred edges, while edge-directed interpolation methods make enlarged images with good quality edges but with detail distortion in the non-edge portion. A new method for constructing a fitting surface to image data is presented. Unlike existing methods which produce enlarged images using image data as interpolation data, the new method constructs the fitting surface using the image data as constraints to reverse the sampling process for improving the fitting precision. To remove the zigzagging artifact, for each pixel and its nearby region, the edge information is used to determine the quadratic polynomial which approximates the original scene with a quadratic polynomial precision. Comparison results of the new method with other methods are included.
Genetic Variation of the Human Urinary Tract Innate Immune Response and Asymptomatic Bacteriuria in Women

Background Although several studies suggest that genetic factors are associated with human UTI susceptibility, the role of DNA variation in regulating early in vivo urine inflammatory responses has not been fully examined. We examined whether candidate gene polymorphisms were associated with altered urine inflammatory profiles in asymptomatic women with or without bacteriuria. Methodology We conducted a cross-sectional analysis of asymptomatic bacteriuria (ASB) in 1,261 asymptomatic women ages 18-49 years originally enrolled as participants in a population-based case-control study of recurrent UTI and pyelonephritis. We genotyped polymorphisms in CXCR1, CXCR2, TLR1, TLR2, TLR4, TLR5, and TIRAP in women with and without ASB. We collected urine samples and measured levels of uropathogenic bacteria, neutrophils, and chemokines. Principal Findings Polymorphism TLR2_G2258A, a variant associated with decreased lipopeptide-induced signaling, was associated with increased ASB risk (odds ratio 3.44, 95%CI; 1.65–7.17). Three CXCR1 polymorphisms were associated with ASB caused by gram-positive organisms. ASB was associated with urinary CXCL-8 levels, but not CXCL-5, CXCL-6, or sICAM-1 (P≤0.0001). Urinary levels of CXCL-8 and CXCL-6, but not ICAM-1, were associated with higher neutrophil levels (P≤0.0001). In addition, polymorphism CXCR1_G827C was associated with increased CXCL-8 levels in women with ASB (P = 0.004). Conclusions TLR2 and CXCR1 polymorphisms were associated with ASB and a CXCR1 variant was associated with urine CXCL-8 levels. These results suggest that genetic factors are associated with early in vivo human bladder immune responses prior to the development of symptomatic UTIs.
Nutrient requirements and growth physiology of the photoheterotrophic Acidobacterium, Chloracidobacterium thermophilum

A novel thermophilic, microaerophilic, anoxygenic, and chlorophototrophic member of the phylum Acidobacteria, Chloracidobacterium thermophilum strain BT, was isolated from a cyanobacterial enrichment culture derived from microbial mats associated with Octopus Spring, Yellowstone National Park, Wyoming. C. thermophilum is strictly dependent on light and oxygen and grows optimally as a photoheterotroph at irradiance values between 20 and 50 μmol photons m-2 s-1. C. thermophilum is unable to synthesize branched-chain amino acids (AAs), l-lysine, and vitamin B12, which are required for growth. Although the organism lacks genes for autotrophic carbon fixation, bicarbonate is also required. Mixtures of other AAs and 2-oxoglutarate stimulate growth. As suggested from genomic sequence data, C. thermophilum requires a reduced sulfur source such as thioglycolate, cysteine, methionine, or thiosulfate. The organism can be grown in a defined medium at 51∘C (Topt; range 44–58∘C) in the pH range 5.5–9.5 (pHopt = ∼7.0). Using the defined growth medium and optimal conditions, it was possible to isolate new C. thermophilum strains directly from samples of hot spring mats in Yellowstone National Park, Wyoming. The new isolates differ from the type strain with respect to pigment composition, morphology in liquid culture, and temperature adaptation.
The korF region of broad-host-range plasmid RK2 encodes two polypeptides with transcriptional repressor activity

Broad-host-range IncP plasmid RK2 possesses a series of operons involved in plasmid maintenance, whose expression is coordinated by a number of regulators, most of which are encoded in the central regulatory korA-korB operon. The nucleotide sequence of two new cistrons in this operon, comprising what we have previously designated the korF locus located between coordinates 57.0 and 56.0 kb on the genome of the IncP alpha plasmid RK2, is presented. The cistrons encode polypeptides of 173 and 175 amino acids. Each can repress transcription from the promoters for the kfrA (a monocistronic operon which follows the korA-korB operon) and trfA (a polycistronic operon encoding a putative single-stranded-DNA-binding protein as well as the essential plasmid replication protein TrfA) operons. In addition, the korF loci allow korB to repress kfrA transcription. Both polypeptides contain hydrophobic segments, suggesting that they may be membrane associated. KorFI is highly basic protein whose predicted properties are similar to those of histone like proteins.
Incremental stability properties for discrete-time systems

Incremental stability describes the asymptotic behavior between any two trajectories of a dynamical system. Such properties are of interest, for example, in the study of observers or synchronization of chaotic systems. In this paper, we develop the notions of incremental stability and incremental input-to-state stability (ISS) for discrete-time systems. We derive Lyapunov function characterizations for these properties as well as a useful summation-to-summation formulation of the incremental stability property.
Collagen type 1 promotes survival of human breast cancer cells by overexpressing Kv10.1 potassium and Orai1 calcium channels through DDR1-dependent pathway

Collagen type 1 is among the tumor microenvironment (TM) factors, that regulates proliferation, survival, migration and invasion. Ion channels are key players in interactions between tumor cells and TM. Kv10.1 has been shown to play an essential role in breast cancer cell proliferation and migration by permitting Ca2+ influx notably via Orai1. Here, we show that human breast cancer (BC) cells growing, in culture media completely devoid of the serum and seeded on collagen 1 coating, exhibited less apoptotic rate and a decrease in Bax expression when compared to those grown on plastic. The survival conferred by collagen 1 was completely abolished by removing extracellular Ca2+ from the culture medium. In addition, Ca2+ entry was increased in collagen 1 condition along with increased Kv10.1 and Orai1 expressions. Moreover, collagen 1 was able to increase co-localization of Kv10.1 and Orai1 on the plasma membrane. Interestingly, silencing of Kv10.1 and Orai1 reduced survival and Ca2+influx without any additive effect. This calcium-dependent survival is accompanied by the activation of ERK1/2, and its pharmacological inhibition completely abolished the increase in Kv10.1 and Orai1 expressions, activities, and the cell survival induced by collagen 1. Moreover, both Kv10.1 and Orai1 knockdown reduced ERK1/2 activation but not Akt. Finally, DDR1 silencing but not β1-integrin reduced the collagen induced survival, ERK1/2 phosphorylation and the expression of Kv10.1 and Orai1. Together these data show that the Kv10.1/Orai1 complex is involved in BC cell survival and this is dependent on collagen 1/DDR1 pathway. Therefore, they represent a checkpoint of tumor progression induced by the tumor microenvironment.
Geometric basis-vector selection methods and subpixel target detection as applied to hyperspectral imagery

In this paper, we compare three basis-vector selection methods as applied to subpixel target detection. This is a continuation of previous research in which a similar comparison was performed based on an AVIRIS image. Our goal is to find out to what extent our previous observations apply more broadly to other images, more specifically, a HYDICE image used in this paper. Our target detection approach is based on generating a radiance target region using a physical model to generate radiance spectra as observed under a wide range of atmospheric, illumination. , and viewing conditions. The advantage of this approach is that the resulting target detection is invariant to those changing conditions. For the purpose of target detection, we use a structured model to describe each image spectra as a linear combination of the target and background basis-vectors, and then we apply a matched subspace detector. Finally, we find ROC curves to describe the relationship between the detection rate (DR) and the false alarm rate (FAR). Due to a large number of cases considered, we use summary metrics to represent our results. The obtained results are quite different from those obtained in (Bajorski et al., 2004) for the AVIRIS image. The best method for generating the background basis vectors in the AVIRIS image was the MaxD method, while the SVD method proved to be best for the HYDICE image used in this paper. Further research is needed to find out the reasons for these differences. It is not surprising that different methods are optimal for different types of data. However, it would be useful to be able to recognize the optimal method without assuming knowledge of the targets in the image
Identification and Characterization of a Gene Cluster for Synthesis of the Polyketide Antibiotic 2,4-Diacetylphloroglucinol from Pseudomonas fluorescens Q2-87

ABSTRACT The polyketide metabolite 2,4-diacetylphloroglucinol (2,4-DAPG) is produced by many strains of fluorescent Pseudomonas spp. with biocontrol activity against soilborne fungal plant pathogens. Genes required for 2,4-DAPG synthesis by P. fluorescensQ2-87 are encoded by a 6.5-kb fragment of genomic DNA that can transfer production of 2,4-DAPG to 2,4-DAPG-nonproducing recipientPseudomonas strains. In this study the nucleotide sequence was determined for the 6.5-kb fragment and flanking regions of genomic DNA from strain Q2-87. Six open reading frames were identified, four of which (phlACBD) comprise an operon that includes a set of three genes (phlACB) conserved between eubacteria and archaebacteria and a gene (phlD) encoding a polyketide synthase with homology to chalcone and stilbene synthases from plants. The biosynthetic operon is flanked on either side by phlEand phlF, which code respectively for putative efflux and regulatory (repressor) proteins. Expression in Escherichia coli of phlA, phlC, phlB, andphlD, individually or in combination, identified a novel polyketide biosynthetic pathway in which PhlD is responsible for the production of monoacetylphloroglucinol (MAPG). PhlA, PhlC, and PhlB are necessary to convert MAPG to 2,4-DAPG, and they also may function in the synthesis of MAPG.
Inhaled Long-acting Anticholinergics and Urinary Tract Infection in Individuals with COPD

ABSTRACT Inhaled, long-acting anticholinergic medication (LAA), commonly used for moderate-to-severe chronic obstructive pulmonary disease (COPD), has been shown to decrease COPD hospitalizations, emergency department visits, and acute exacerbations but has also been associated with urinary tract infection (UTI) in a prior meta-analysis. The objective of this study was to verify if there was an association between LAA and UTI in older individuals with COPD. A population-based, real-world cohort study using health administrative data from Ontario, Canada was conducted. Incidence of UTI was compared between older people with physician-diagnosed COPD, who were new users of inhaled long-acting anticholinergics and new users of inhaled corticosteroids–a reference medication used in similar clinical settings that has no known association with UTI. Propensity score matching was used to minimize the effects of confounding. An overall association between LAA and various measures of UTI in older individuals was not found. However, in a priori defined stratified analyses, men newly initiated on LAA were 75% more likely to develop a UTI than men newly started on an inhaled corticosteroid (hazard ratio 1.75; 95% confidence interval 1.05–2.92). No significant association was seen in women. In conclusion, older men with COPD newly started on LAA are at increased risk of UTI. Men considering an inhaled LAA should be informed of this risk and, if they decide to take it, be provided with appropriate monitoring.
The Association of Low-To-Moderate Alcohol Consumption with Breast Cancer Subtypes Defined by Hormone Receptor Status

Background Alcohol is a well-established risk factor for breast cancer, but pathways involved in alcohol-related breast carcinogenesis are not clearly defined. We examined the association between low-to-moderate alcohol intake and breast cancer subtypes by tumor hormone receptor status. Materials and Methods A hospital-based case-control study was performed in 585 cases and 1,170 controls. Information on alcohol intake and other risk factors was collected via a questionnaire. Logistic regression was used for analyses. All statistical tests were two-sided. Results The odds ratio of breast cancer was 1.75 (95% confidence interval [CI]: 1.21–2.53) in women who consumed ≤5 drinks/week, and 3.13 (95% CI: 1.81–5.43) in women who consumed >5 drinks/week, both compared with non-drinkers for ≥10 years, after adjustment for age and other confounders. The association of alcohol intake with estrogen receptor-positive breast cancer was stronger than with estrogen receptor-negative: the odds ratio per 1 category increase was 2.05 (95% CI: 1.49–2.82) and 1.29 (95% CI: 0.85–1.94) (P-heterogeneity = 0.07). There was no evidence of an interaction between alcohol intake and menopausal status (P = 0.19) in overall group; however, it was significant in estrogen receptor-positive breast cancer (P = 0.04). Conclusions Low-to-moderate alcohol intake is associated with the risk of estrogen receptor-positive breast cancer with the strongest association in postmenopausal women. Since alcohol intake is a modifiable risk factor of breast cancer, every woman should be informed and advised to control alcohol use.
Effects of a Short-Term High-Nitrate Diet on Exercise Performance

It has been reported that nitrate supplementation can improve exercise performance. Most of the studies have used either beetroot juice or sodium nitrate as a supplement; there is lack of data on the potential ergogenic benefits of an increased dietary nitrate intake from a diet based on fruits and vegetables. Our aim was to assess whether a high-nitrate diet increases nitric oxide bioavailability and to evaluate the effects of this nutritional intervention on exercise performance. Seven healthy male subjects participated in a randomized cross-over study. They were tested before and after 6 days of a high (HND) or control (CD) nitrate diet (~8.2 mmol∙day−1 or ~2.9 mmol∙day−1, respectively). Plasma nitrate and nitrite concentrations were significantly higher in HND (127 ± 64 µM and 350 ± 120 nM, respectively) compared to CD (23 ± 10 µM and 240 ± 100 nM, respectively). In HND (vs. CD) were observed: (a) a significant reduction of oxygen consumption during moderate-intensity constant work-rate cycling exercise (1.178 ± 0.141 vs. 1.269 ± 0.136 L·min−1); (b) a significantly higher total muscle work during fatiguing, intermittent sub-maximal isometric knee extension (357.3 ± 176.1 vs. 253.6 ± 149.0 Nm·s·kg−1); (c) an improved performance in Repeated Sprint Ability test. These findings suggest that a high-nitrate diet could be a feasible and effective strategy to improve exercise performance.
System-level timing analysis and scheduling for embedded packet processors

Packet processors are high-performance, programmable devices with special architectural features that are optimized for network packet processing. They are mostly embedded within network routers and switches and are designed to implement complex packet processing tasks at high line speeds. In this thesis we study several issues related to system-level timing analysis and scheduling for such embedded packet processors. Our work is motivated by the fact that designing and analysing the hardware-software architectures for packet processors require new models and methods which do not fall within the preview of traditionally studied embedded systems. Both, timing analysis and scheduling have been widely studied in the context of system-level design of embedded systems. But most of these studies have either focussed on purely data-dominated applications like digital signal and image processing, or on purely control-dominated applications such as those found in automobile control systems or in appliances like washing machines and microwave ovens. Packet-processing applications, on the other hand, combine features from both these domains and additionally have several new characteristics and requirements. Their design also requires an integration of concepts from several areas, such as embedded systems, computer architecture and networking. As a result, the design and analysis of packet processors are not sufficiently supported by current high-level design methodologies and tools targeted towards embedded-systems design. This thesis partially fills this gap by proposing new models and algorithms specifically directed towards designing network packet processors, and makes the following main contributions. Packet processors typically consist of a collection of heterogeneous processing elements, which are required to process multiple packet flows at line speed. We pose the problem of determining the feasibility of a mapping of the different packet-processing tasks onto the different processing elements, as a schedulability analysis problem. It turns out that for the task model we consider, this schedulability analysis problem is intractable (NP-hard) and therefore can not be solved within any reasonable time. To get around this, we introduce a novel concept called “approximate schedulability analysis”, using which the problem can be solved in polynomial time if a small error in the decisions made by the algorithm is allowed. Using this concept, we demonstrate that in spite of the intractability result, a schedulability analysis can nevertheless be done in reasonable time for all practical purposes. We also show that this concept is not
Are Suicide Attempters Who Self-mutilate a Unique Population?

Objective: Individuals who mutilate themselves are at greater risk for suicidal behavior. Clinically, however, there is a perception that the suicide attempts of self-mutilators are motivated by the desire for attention rather than by a genuine wish to die. The purpose of this study was to determine differences between suicide attempters with and without a history of self-mutilation. Method: The authors examined demographic characteristics, psychopathology, objective and perceived lethality of suicide attempts, and perceptions of their suicidal behavior in 30 suicide attempters with cluster B personality disorders who had a history of self-mutilation and a matched group of 23 suicide attempters with cluster B personality disorders who had no history of self-mutilation. Results: The two groups did not differ in the objective lethality of their attempts, but their perceptions of the attempts differed. Self-mutilators perceived their suicide attempts as less lethal, with a greater likelihood of rescue and with less certainty of death. In addition, suicide at-tempters with a history of self-mutilation had significantly higher levels of depression , hopelessness, aggression, anxiety, impulsivity, and suicide ideation. They exhibited more behaviors consistent with borderline personality disorder and were more likely to have a history of childhood abuse. Self-mutilators had more persistent suicide ideation, and their pattern for suicide was similar to their pattern for self-mutilation, which was characterized by chronic urges to injure themselves. Conclusions: Suicide attempters with cluster B personality disorders who have a history of self-mutilation tend to be more depressed, anxious, and impulsive, and they also tend to underestimate the lethality of their suicide attempts. Therefore , clinicians may be unintentionally misled in assessing the suicide risk of self-mutilators as less serious than it is. Sel f-mutilation is deliberate self-harm without the intent to die. The most usual forms are cutting and burning (1, 2). Individuals with borderline personality disorder who have a history of self-mutilation are at much greater risk of death by suicide. Self-mutilation occurs most often in the context of borderline personality disorder (3), which carries a lifetime suicide rate of 5%–10% (4–6). Approximately 55%–85% of self-mutilators have made at least one suicide attempt (7–12). Despite these substantial morbidity and mortality rates, the purpose of suicidal behavior in these individuals has been described as not " genuinely " suicidal or life-threatening (13) but primarily attention-seeking and manipulative. However, it is questionable to view this behavior as nonserious because up to 10% of this population commits …
Bottom-up and Top-down Control in Visual Search

Previous research suggests that the allocation of attention is largely controlled either in a stimulus-driven or in a goal-driven manner. To date, few studies have systematically manipulated variables affecting stimulus-driven and goal-driven selection independently in order to investigate how both manners of control interrelate and affect performance in visual search. In the present study observers were presented with search displays consisting of an array of line segments rotated at various orientations. The task of observers was to indicate the presence or absence of a vertical line segment (the target) presented amongst a series of nontargets and possibly one distractor. By varying the absolute differences in orientation between the target, nontargets, and distractors, relative target–distractor salience and target–distractor similarity were independently manipulated to investigate the contribution of stimulus-driven and goal-driven control. The major result was that relative target–distractor salience and target–distractor similarity affected search performance independently. Performance was better in cases where the irrelevant distractor was not a salient item in the search display and did not look similar to the target. The results are discussed in terms of models of attentional control.