Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional luminal imaging probe topography: an improved method for characterizing esophageal distensibility in eosinophilic esophagitis

Objectives: The aims of this study were to develop a new method for analysis and presentation of esophageal distensibility data using high-resolution impedance planimetry recordings during a volume-controlled distention. Methods: Two control subjects and six patients with eosinophilic esophagitis (EoE) with stricture, narrow caliber or normal endoscopy according to EndoFLIP studies were included for analysis. Median filtering and pulse detection techniques were applied to the pressure signal and a wavelet decomposition technique was applied to the 16 channels of raw esophageal diameter data to reduce vascular artifact, respiratory effect and remove esophageal contraction interference. These data were used to generate a functional luminal imaging probe (FLIP) topography plot that describes regional variation of cross-sectional area (CSA). A previously developed computer program was used to calculate and model the CSA-pressure data to derive the slope of line fitting and distension plateau for each individual subject. The results were compared among the four endoscopic phenotypes. Results: Patients with EoE and normal endoscopy had similar esophageal distensibility parameters to those of normal controls whereas patients with EoE and stricture or narrow caliber had much lower distensibility than patients with EoE and normal endoscopy. The FLIP topography plots provided a global assessment of the esophageal distensibility along the axial plane of measurement that differentiated patients with varying degrees of endoscopic abnormality. Conclusions: New techniques can be leveraged to improve data analysis and presentation using EndoFLIP assessment of the esophageal body in EoE. These techniques may be helpful in defining clinically relevant phenotypes and guiding treatment strategies and should be helpful in structuring future outcome trials.
Cooperative willingness perception based routing algorithm in opportunistic network

There is a cooperative willingness perception based routing algorithm is proposed in this paper. The average duration of messages forwarding is utilized to measure the cooperative willingness between nodes; moreover, combining with the parameter of contact probability between nodes, the relay node can be selected reasonably. Further, in order to maximize the utility of network resources, message priority is considered. Results show that the proposed algorithm can effectively improve network performance.
Quantification of essential tremor in writing and drawing

Eighty‐seven patients, aged 15–84 years (mean, 61.8 ± 16.2 SD), with essential tremor wrote two series of cursive e's and cursive l's on a standard sheet of ruled paper that was mounted on a commercially available digitizing tablet. Forty patients also drew an Archimedes spiral. Postural wrist tremor was measured with a triaxial accelerometer on the dorsum of the horizontally extended hand. The digitizing tablet was sufficiently sensitive to measure sustained visible tremor. Very severe tremor could not be recorded when it prevented a patient from keeping the ballpoint pen on the tablet. The intertrial variability of the handwriting data was such that a 36.0% change in mean acceleration amplitude (cm/s2) and an 8.3% change in mean tremor frequency (Hz) could be detected in a hypothetical population of 30 patients (paired‐sample t test, p = 0.01, power = 90%). The intertrial changes detectable with accelerometry were 35.9% (amplitude) and 7.8% (frequency). The correlations between wrist tremor and writing tremor were <0.60 for amplitude and <0.25 for frequency. Significant correlations between patient age and tremor frequency and between tremor amplitude and frequency existed for postural tremor but not for writing or drawing tremor. Standard digitizing tablets for personal computers are useful in the quantitative assessment of writing tremor. The amplitude and frequency characteristics of tremor in posture, writing, and drawing may differ significantly.
Smoking cessation interventions with female smokers living with HIV/AIDS: A randomized pilot study of motivational interviewing

Smoking among people living with HIV, particularly women living with HIV, is associated with higher morbidity and mortality rates when compared to nonsmoking individuals with HIV. Despite patients’ higher risk of adverse health outcomes, in particular preventable smoking-related diseases for smokers living with HIV, few smoking cessation interventions have been examined with this population. The aim of the current study was to test the potential efficacy of a brief motivational intervention for smoking cessation with HIV-infected women smokers. Participants (N=30) were randomly assigned to receive a single session of motivational interviewing (MI) or prescribed advice (PA). The primary outcome was seven-day point prevalence abstinence at the one-month follow-up interview. Secondary outcome measures included mean cigarettes smoked per day, desire to quit smoking, perceived difficulty in quitting smoking, and expectation of success. We detected no significant differences between intervention and control groups in self-reported seven-day point prevalence abstinence at the one-month follow-up. However, participants in the MI condition reported a significant decrease in the mean cigarettes smoked per day when compared to the PA condition. There were no significant between-group differences in participants’ desire to quit, perceived difficulty, and expectation of success. The results of this pilot study indicate that MI may be an effective smoking cessation intervention for HIV-positive women smokers and should be studied further in a larger clinical trial.
Hsp90/Hsp70 Chaperone Machine Regulation of the Saccharomyces MAL-Activator As Determined in Vivo Using Noninducible and Constitutive Mutant Alleles

The Hsp90/Hsp70 chaperone machine is an essential regulator of cell growth and division. It is required for activation of select client proteins, chiefly protein kinases and transcription activators and thus plays a major role in regulating intracellular signaling and gene expression. This report demonstrates, in vivo, the association of the Saccharomyces cerevisiae maltose-responsive transcription activator Mal63 (MAL-activator) with the yeast Hsp70 (Ssa1), Hsp90 (Hsp82), and Hop (Sti1) homologs, using a collection of inducible, constitutive, and noninducible alleles. Each class of mutant activator forms a distinctly different stable multichaperone complex in the absence of maltose. Inducible Mal63p associates with Ssa1, Hsp82, and Sti1 and is released in the presence of maltose. Noninducible mal63 mutant proteins bind to Ssa1 alone and do not stably associate with Hsp82 or Sti1. Constitutive MAL-activators bind well to Hsp82 and poorly to Ssa1 and Sti1, but deletion of STI1 restores Ssa1 binding. Taken together, Mal63p regulation requires the formation of Hsp90/Hsp70 subcomplexes comparable to, yet distinct from those observed with previously characterized Hsp90 clients including glucocorticoid receptor and yeast Hap1p. Thus, comparative studies of different client proteins highlight functional diversity in the operation of the Hsp90/Hsp70 chaperone machine.
Multi-walled carbon nanotubes: sampling criteria and aerosol characterization

This study intends to develop protocols for sampling and characterizing multi-walled carbon nanotube (MWCNT) aerosols in workplaces or during inhalation studies. Manufactured dry powder containing MWCNT’s, combined with soot and metal catalysts, form complex morphologies and diverse shapes. The aerosols, examined in this study, were produced using an acoustical generator. Representative samples were collected from an exposure chamber using filters and a cascade impactor for microscopic and gravimetric analyses. Results from filters showed that a density of 0.008–0.10 particles per µm2 filter surface provided adequate samples for particle counting and sizing. Microscopic counting indicated that MWCNT’s, resuspended at a concentration of 10 mg/m3, contained 2.7 × 104 particles/cm3. Each particle structure contained an average of 18 nanotubes, resulting in a total of 4.9 × 105 nanotubes/cm3. In addition, fibrous particles within the aerosol had a count median length of 3.04 µm and a width of 100.3 nm, while the isometric particles had a count median diameter of 0.90 µm. A combination of impactor and microscopic measurements established that the mass median aerodynamic diameter of the mixture was 1.5 µm. It was also determined that the mean effective density of well-defined isometric particles was between 0.71 and 0.88 g/cm3, and the mean shape factor of individual nanotubes was between 1.94 and 2.71. The information obtained from this study can be used for designing animal inhalation exposure studies and adopted as guidance for sampling and characterizing MWCNT aerosols in workplaces. The measurement scheme should be relevant for any carbon nanotube aerosol.
Morphology, Genome Sequence, and Structural Proteome of Type Phage P335 from Lactococcus lactis

ABSTRACT Lactococcus lactis phage P335 is a virulent type phage for the species that bears its name and belongs to the Siphoviridae family. Morphologically, P335 resembled the L. lactis phages TP901-1 and Tuc2009, except for a shorter tail and a different collar/whisker structure. Its 33,613-bp double-stranded DNA genome had 50 open reading frames. Putative functions were assigned to 29 of them. Unlike other sequenced genomes from lactococcal phages belonging to this species, P335 did not have a lysogeny module. However, it did carry a dUTPase gene, the most conserved gene among this phage species. Comparative genomic analyses revealed a high level of identity between the morphogenesis modules of the phages P335, ul36, TP901-1, and Tuc2009 and two putative prophages of L. lactis SK11. Differences were noted in genes coding for receptor-binding proteins, in agreement with their distinct host ranges. Sixteen structural proteins of phage P335 were identified by liquid chromatography-tandem mass spectrometry. A 2.8-kb insertion was recognized between the putative genes coding for the activator of late transcription (Alt) and the small terminase subunit (TerS). Four genes within this region were autonomously late transcribed and possibly under the control of Alt. Three of the four deduced proteins had similarities with proteins from Streptococcus pyogenes prophages, suggesting that P335 acquired this module from another phage genome. The genetic diversity of the P335 species indicates that they are exceptional models for studying the modular theory of phage evolution.
Hypothesis Validation of Far-Wall Brightness in Carotid-Artery Ultrasound for Feature-Based IMT Measurement Using a Combination of Level-Set Segmentation and Registration

Intima-media thickness (IMT) is now being considered as an indicator of atherosclerosis. Our group has developed several feature-based IMT measurement algorithms such as the Completely Automated Layer EXtraction (CALEX) (which is a class of patented AtheroEdge Systems from Global Biomedical Technologies, Inc., CA, USA). These methods are based on the hypothesis that the highest pixel intensities are in the far wall of the common carotid artery (CCA) or the internal carotid artery (ICA). In this paper, we verify that this hypothesis holds true for B-mode longitudinal ultrasound (US) images of the carotid wall. This patented methodology consists of generating the composite image (the arithmetic sum of images) from the database by first registering the carotid image frames with respect to a nearly straight carotid-artery frame from the same database using: (1) B-spline-based nonrigid registration and (2) affine registration. Prior to registration, we segment the carotid-artery lumen using a level-set-based algorithm followed by morphological image processing. The binary lumen images are registered, and the transformations are applied to the original grayscale CCA images. We evaluated our technique using a database of 200 common carotid images of normal and pathologic carotids. The composite image presented the highest intensity distribution in the far wall of the CCA/ICA, validating our hypothesis. We have also demonstrated the accuracy and improvement in the IMT segmentation result with our CALEX 3.0 system. The CALEX system, when run on newly acquired US images, shows the IMT error of about 30 μm. Thus, we have shown that the CALEX algorithm is able to exploit the far-wall brightness for accurate IMT measurements.
Reductive Activation of Type 2 Ribosome-inactivating Proteins Is Promoted by Transmembrane Thioredoxin-related Protein*

Background: PDI is implicated in the intracellular reduction of ricin; other oxidoreductases also have a role in this process. Results: Overexpression and silencing of TMX affect ricin cytotoxicity. Conclusion: TMX participates with PDI and/or other reductases in the reduction of ricin and other proteins. Significance: These findings contribute to the understanding of disulfide reduction in cell intoxication by toxins and virus assembly and entry. Members of the type 2 ribosome-inactivating proteins (RIPs) family (e.g. ricin, abrin) are potent cytotoxins showing a strong lethal activity toward eukaryotic cells. Type 2 RIPs contain two polypeptide chains (usually named A, for “activity”, and B, for “binding”) linked by a disulfide bond. The intoxication of the cell is a consequence of a reductive process in which the toxic domain is cleaved from the binding domain by oxidoreductases located in the lumen of the endoplasmic reticulum (ER). The best known example of type 2 RIPs is ricin. Protein disulfide isomerase (PDI) was demonstrated to be involved in the process of ricin reduction; however, when PDI is depleted from cell fraction preparations ricin reduction can still take place, indicating that also other oxidoreductases might be implicated in this process. We have investigated the role of TMX, a transmembrane thioredoxin-related protein member of the PDI family, in the cell intoxication operated by type 2 RIPs ricin and abrin. Overexpressing TMX in A549 cells resulted in a dramatic increase of ricin or abrin cytotoxicity compared with control mock-treated cells. Conversely, no difference in cytotoxicity was observed after treatment of A549 cells or control cells with saporin or Pseudomonas exotoxin A whose intracellular mechanism of activation is not dependent upon reduction (saporin) or only partially dependent upon it (Pseudomonas exotoxin A). Moreover, the silencing of TMX in the prostatic cell line DU145 reduced the sensitivity of the cells to ricin intoxication further confirming a role for this enzyme in intracellular ricin activation.
Evolvable social agents for bacterial systems modeling

We present two approaches to the individual-based modeling (IbM) of bacterial ecologies and evolution using computational tools. The IbM approach is introduced, and its important complementary role to biosystems modeling is discussed. A fine-grained model of bacterial evolution is then presented that is based on networks of interactivity between computational objects representing genes and proteins. This is followed by a coarser grained agent-based model, which is designed to explore the evolvability of adaptive behavioral strategies in artificial bacteria represented by learning classifier systems. The structure and implementation of the two proposed individual-based bacterial models are discussed, and some results from simulation experiments are presented, illustrating their adaptive properties.
GT160-246, a Toxin Binding Polymer for Treatment ofClostridium difficile Colitis

ABSTRACT GT160-246, a high-molecular-weight soluble anionic polymer, was tested in vitro and in vivo for neutralization of Clostridium difficile toxin A and B activities. Five milligrams of GT160-246 per ml neutralized toxin-mediated inhibition of protein synthesis in Vero cells induced by 5 ng of toxin A per ml or 1.25 ng of toxin B per ml. In ligated rat ileal loops, 1 mg of GT160-246 neutralized fluid accumulation caused by 5 μg of toxin A. At doses as high as 80 mg/loop, cholestyramine provided incomplete neutralization of fluid accumulation caused by 5 μg of toxin A. GT160-246 protected 80% of the hamsters from mortality caused by infection with C. difficile, whereas cholestyramine protected only 10% of animals. Treatment of C. difficile-infected hamsters with metronidazole initially protected 100% of the hamsters from mortality, but upon removal of treatment, 80% of the hamsters had relapses and died. In contrast, removal of GT160-246 treatment did not result in disease relapse in the hamsters. GT160-246 showed no antimicrobial activity in tests with a panel of 16 aerobic bacteria and yeast and 22 anaerobic bacteria and did not interfere with the in vitro activities of most antibiotics. GT160-246 offers a novel, nonantimicrobial treatment of C. difficile disease in humans.
Coping and Distress: What Happens After Intervention? A 2-Year Follow-up From the Swedish Obese Subjects (SOS) Study

Objective The study examined effects of weight change on coping and distress in severely obese subjects treated conventionally or undergoing weight reduction surgery. Methods We used the Obesity Coping (OC) scale measuring emotion-focused, maladaptive coping (Wishful Thinking) and problem-focused, adaptive coping (Social Trust and Fighting Spirit). We also used the Obesity Distress (OD) scale (Intrusion and Helplessness) and the Hospital Anxiety and Depression (HAD) scale. A total of 1146 surgical candidates and 1085 conventionally treated patients completed the OC and OD before treatment and after 24 months. Results Weight gainers reduced their use of both problem- and emotion-focused coping, thus leaving distress levels unchanged. All participants who lost weight decreased in emotion-focused coping and distress. Participants losing 20 kg or more also increased in problem-focused coping, resulting in even greater improvements regarding distress. Conclusions Two years after starting treatment, the pattern and magnitude of change in coping and distress was the same irrespective of type of treatment and was, instead, related to the amount of weight change (the more weight change the greater the changes in coping and distress). Increases in problem-focused coping required major weight reduction, whereas minor weight gain led to a decrease. Emotion-focused coping decreased irrespective of direction of weight change, suggesting a general intervention effect of receiving professional help and support. These results have implications concerning behavior-based interventions of obese patients.
Head‐to‐head comparison between delayed enhancement and percent infarct mapping for assessment of myocardial infarct size in a canine model

To compare a novel method, percent‐infarct‐mapping (PIM), with conventional delayed enhancement (DE) of contrast for accurate myocardial viability assessment. Contrary to signal intensity (SI), the longitudinal relaxation‐rate enhancement (ΔR1) is an intrinsic parameter linearly proportional to the concentration of contrast agent (CA). Determining ΔR1 voxel‐by‐voxel, after administering an infarct‐avid CA, allows determination of per‐voxel percentage of infarcted tissue. The feasibility of generating PIM is demonstrated in canine reperfused infarction using an infarct‐avid, persistent‐CA (PCA), (Gd)(ABE‐DTTA). PIM is compared to the DE method using Gd(DTPA), and both to triphenyltetrazolium chloride (TTC) staining histochemistry.
Robust Toll Pricing

We study a robust toll pricing problem where toll setters and users have different level of information when taking their decisions. Toll setters do not have full information on the costs of the network and rely on historical information when determining toll rates, whereas users decide on the path to use from origin to destination knowing toll rates and having, in addition, more accurate traffic data. In this work, we first consider a single origin-destination parallel network and formulate the robust toll pricing problem as a distributionally robust optimization problem, for which we develop an exact algorithm based on a mixed-integer programming formulation and a heuristic based on two-point support distribution. We further extend our formulations to more general networks and show how our algorithms can be adapted for the general networks. Finally, we illustrate the usefulness of our approach by means of numerical experiments both on randomly generated networks and on the road network of the city of Chicago.
Is There Asymmetric Price Transmission in the U.S. Fluid Milk Market

This study is used to examine the characteristics of the retail price adjustment within the U.S. fluid whole milk market. We employ an error correction model (ECM) to test for asymmetry in the transmission of farm milk price changes to changes in the retail price. In this analysis we use monthly data of farm and retail whole milk prices encompassing the January 2001 to December 2011 period for 16 U.S. cities. Several cities were found to display asymmetric price transmission where retail prices tended to respond more quickly with farm price increases vs. decreases.
Impact of NBTI and PBTI in SRAM bit-cells: Relative sensitivities and guidelines for application-specific target stability/performance

The stability and performance characteristics of Static Random Access Memories (SRAMs) are known to degrade with time due to the impact of Negative and Positive Bias Temperature Instabilities (NBTI (in PFET) and PBTI (in NFET)). In this work, we provide insights into relative sensitivities of these phenomena on speed and stability of SRAM cells. Relative impact on access time, stability, and tolerability of one phenomenon over another has been studied for different application specific (high-performance or low-power) SRAM cells. We show that high-performance SRAM cells should have lower VT drift due to PBTI compared with dense cells to contain READ stability and access time. Further, worst-case static stress poses tighter process constraints compared with alternating stress.
Are Patriots Bigots? An Inquiry into the Vices of In-Group Pride

One view in the study of intergroup conflict is that pride implies prejudice. However, an increasing number of scholars have come to view in-group pride more benignly, suggesting that such pride can be accompanied by a full range of feelings toward the out-group. In this article, we focus on a substantively interesting case of in-group/out-group attitudes—national pride and hostility toward immigrants. We explore the relationship in two fundamental ways: first by examining the prejudice associated with various dimensions of pride, and second by embedding these relationships in a comprehensive model of prejudice. We find that national pride is most validly measured with two dimensions—patriotism and nationalism—two dimensions that have very different relationships with prejudice. While nationalists have a strong predilection for hostility toward immigrants, patriots show no more prejudice than does the average citizen.