Miracle-dz/UniFAR-FTUs huggingface dataset:
Social Network, Surgeon, and Media Influence on the Decision to Undergo Contralateral Prophylactic Mastectomy

Objectives: The rate of contralateral prophylactic mastectomy (CPM) has risen sharply in the past decade. The current study was designed to examine social network, surgeon, and media influence on patients’ CPM decision-making, examining not only who influenced the decision, and to what extent, but also the type of influence exerted. Methods: Patients (N=113) who underwent CPM at 4 Indiana University–affiliated hospitals between 2008 and 2012 completed structured telephone interviews in 2013. Questions addressed the involvement and influence of the social network (family, friends, and nonsurgeon health professionals), surgeon, and media on the CPM decision. Results: Spouses, children, family, friends, and health professionals were reported as exerting a meaningful degree of influence on patients’ decisions, largely in ways that were positive or neutral toward CPM. Most surgeons were regarded as providing options rather than encouraging or discouraging CPM. Media influence was present, but limited. Conclusions: Patients who choose CPM do so with influence and support from members of their social networks. Reversing the increasing choice of CPM will require educating these influential others, which can be accomplished by encouraging patients to include them in clinical consultations, and by providing patients with educational materials that can be shared with their social networks. Surgeons need to be perceived as having an opinion, specifically that CPM should be reserved for those patients for whom it is medically indicated.
Multiple Pathways of Plasmid DNA Transfer in Helicobacter pylori

Many Helicobacter pylori (Hp) strains carry cryptic plasmids of different size and gene content, the function of which is not well understood. A subgroup of these plasmids (e.g. pHel4, pHel12), contain a mobilisation region, but no cognate type IV secretion system (T4SS) for conjugative transfer. Instead, certain H. pylori strains (e.g. strain P12 carrying plasmid pHel12) can harbour up to four T4SSs in their genome (cag-T4SS, comB, tfs3, tfs4). Here, we show that such indigenous plasmids can be efficiently transferred between H. pylori strains, even in the presence of extracellular DNaseI eliminating natural transformation. Knockout of a plasmid-encoded mobA relaxase gene significantly reduced plasmid DNA transfer in the presence of DNaseI, suggesting a DNA conjugation or mobilisation process. To identify the T4SS involved in this conjugative DNA transfer, each individual T4SS was consecutively deleted from the bacterial chromosome. Using a marker-free counterselectable gene deletion procedure (rpsL counterselection method), a P12 mutant strain was finally obtained with no single T4SS (P12ΔT4SS). Mating experiments using these mutants identified the comB T4SS in the recipient strain as the major mediator of plasmid DNA transfer between H. pylori strains, both in a DNaseI-sensitive (natural transformation) as well as a DNaseI-resistant manner (conjugative transfer). However, transfer of a pHel12::cat plasmid from a P12ΔT4SS donor strain into a P12ΔT4SS recipient strain provided evidence for the existence of a third, T4SS-independent mechanism of DNA transfer. This novel type of plasmid DNA transfer, designated as alternate DNaseI-Resistant (ADR) mechanism, is observed at a rather low frequency under in vitro conditions. Taken together, our study describes for the first time the existence of three distinct pathways of plasmid DNA transfer between H. pylori underscoring the importance of horizontal gene transfer for this species.
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Humanoid Gait Optimization Based on Human Data

Achieving a stable, human-like gait for humanoid robots is a challenging task. While a variety of techniques exist to generate stable walking patterns, only little attention has been paid to the resemblance to the human gait. Popular gaits, for example, apply the strategy to bend the knees and to swing the torso in the lateral direction in order to ensure stability by shifting the center of mass. As a result, the walking patterns do not look very humanlike. However, human resemblance is an important aspect whenever robots are designed to coexist and interact with humans. In this article, we present techniques to optimize a given, stable gait of a humanoid robot with respect to human resemblance. To acquire human data, we use a full-body motion capture system. We propose four different optimization algorithms that work at joint angle basis and use the joint angle difference as measure of similarity. The experiments carried out with a HOAP-2 robot in simulation demonstrate that all techniques generate a gait that is significantly more human-like compared to the robot's initial gate. As the results show, the optimization methods based on hill climbing and policy gradient estimation yield the best performance.
Modeling User Networks in Recommender Systems

Recommender systems, in the collaborative filtering variation, are popular tools used to drive users out of information clutter, by letting them select ¿interesting¿ items based on the preferences of similarly minded users. In such a system as more users come in to evaluate items (be they information pieces, products or otherwise), a network of users starts to be formed. In this paper we are interested in the dynamics of such a network, in particular we investigate if there is a hidden law that captures the essence of such networks irrespective of their size. The discovery of such a law would allow, among other usages, generation of synthetic data sets, realistic enough to be used for simulation purposes. Furthermore, it would be useful for information-seeking activities such as locating known experts or influential users on a particular subject. Similar work in related fields suggested the existence of power-laws, which seem to be ubiquitous. However, in our work we did not detect the presence of such a law, instead we discovered an exponential relationship between the nodes of a graph representing users, and edges representing similarity between users. In particular the logarithm of the degree of node is linearly related to the ranking of the node in a decreasing order. The above conclusion is justified by extended experiments on two versions of the movie lens data set (one comprised 100,000 user evaluations, while the other comprised 1,000,0000 evaluations).
Randomised placebo controlled trial of non-invasive ventilation for hypercapnia in cystic fibrosis

Background: The clinical benefits of domiciliary non-invasive positive pressure ventilation (NIV) have not been established in cystic fibrosis (CF). We studied the effects of nocturnal NIV on quality of life (QoL), functional and physiological outcomes in CF subjects with awake hypercapnia (arterial carbon dioxide pressure Paco2>45 mm Hg). Methods: In a randomised, placebo controlled, crossover study, eight subjects with CF, mean (SD) age 37 (8) years, body mass index 21.1 (2.6) kg/m2, forced expiratory volume in 1 s 35 (8)% predicted and Paco2 52 (4) mm Hg received 6 weeks of nocturnal (1) air (placebo), (2) oxygen and (3) NIV. The primary outcome measures were CF specific QoL, daytime sleepiness and exertional dyspnoea. Secondary outcome measures were awake and asleep gas exchange, sleep architecture, lung function and peak exercise capacity. Results: Compared with air, NIV improved the chest symptom score in the CF QoL Questionnaire (mean difference 10; 95% CI 5 to 16; p = 0.002) and the transitional dyspnoea index score (mean difference 3.1; 95% CI 1.2–5.0; p = 0.01). It reduced maximum nocturnal pressure of transcutaneous CO2 (Ptcco2 mean difference −17 mm Hg; 95% CI −7 to −28 mm Hg; p = 0.005) and increased exercise performance on the Modified Shuttle Test (mean difference 83 m; 95% CI 21 to 144 m; p = 0.02). NIV did not improve sleep architecture, lung function or awake Paco2. Conclusion: 6 weeks of nocturnal NIV improves chest symptoms, exertional dyspnoea, nocturnal hypoventilation and peak exercise capacity in adult patients with stable CF with awake hypercapnia. Further studies are required to determine whether or not NIV can improve survival.
HIV-1 Protease: Structural Perspectives on Drug Resistance

Antiviral inhibitors of HIV-1 protease are a notable success of structure-based drug design and have dramatically improved AIDS therapy. Analysis of the structures and activities of drug resistant protease variants has revealed novel molecular mechanisms of drug resistance and guided the design of tight-binding inhibitors for resistant variants. The plethora of structures reveals distinct molecular mechanisms associated with resistance: mutations that alter the protease interactions with inhibitors or substrates; mutations that alter dimer stability; and distal mutations that transmit changes to the active site. These insights will inform the continuing design of novel antiviral inhibitors targeting resistant strains of HIV.
A Silicon Monolithic Phase-Inverter Rat-Race Coupler Using Spiral Coplanar Striplines and Its Application in a Broadband Gilbert Mixer

This paper realized a broadband uniplanar phase-inverter rat-race coupler using a standard silicon process, and then analyzed this coupler under a lossy condition. A phase inverter is employed in this coupler, not only to extend the operation bandwidth, but also to generate balanced outputs by providing equal lossy paths, while symmetrical spiral-shaped coplanar striplines (CPSs) are also utilized to shrink the coupler size, as well as to construct a phase inverter in the middle of one of spiral CPSs. The lossy CPS, when designed as a distortionless line, has a real characteristic impedance, and thus, perfect port matching of the coupler can be achieved at the center frequency. The operation frequency of this silicon monolithic rat-race coupler with the size of 0.5 mm2 is extremely wide and ranges from 5 to 23 GHz. The dissipated loss, transmission coefficient, and isolation of the rat- race coupler are approximately 5.5, -8, and below -25 dB, respectively. In addition, a wideband Gilbert micromixer with an integrated uniplanar phase-inverter rat-race coupler at the local oscillator port is demonstrated using 0.35-mum SiGe BiCMOS technology. This mixer works from 2.5 to 13 GHz with 12-dB conversion gain, -16-dBm IP1 dB, -4-dBm IIP3, and 14-dB noise figure. The chip size of the mixer with an integrated coupler is approximately 1.4 mm times 1.4 mm.
A Neural Mechanism for Microsaccade Generation in the Primate Superior Colliculus

During fixation, the eyes are not still but often exhibit microsaccadic movements. The function of microsaccades is controversial, largely because the neural mechanisms responsible for their generation are unknown. Here, we show that the superior colliculus (SC), a retinotopically organized structure involved in voluntary-saccade target selection, plays a causal role in microsaccade generation. Neurons in the foveal portion of the SC increase their activity before and during microsaccades with sizes of only a few minutes of arc and exhibit selectivity for the direction and amplitude of these movements. Reversible inactivation of these neurons significantly reduces microsaccade rate without otherwise compromising fixation. These results, coupled with computational modeling of SC activity, demonstrate that microsaccades are controlled by the SC and explain the link between microsaccades and visual attention.
Plant-Polysaccharide-Degrading Enzymes from Basidiomycetes

SUMMARY Basidiomycete fungi subsist on various types of plant material in diverse environments, from living and dead trees and forest litter to crops and grasses and to decaying plant matter in soils. Due to the variation in their natural carbon sources, basidiomycetes have highly varied plant-polysaccharide-degrading capabilities. This topic is not as well studied for basidiomycetes as for ascomycete fungi, which are the main sources of knowledge on fungal plant polysaccharide degradation. Research on plant-biomass-decaying fungi has focused on isolating enzymes for current and future applications, such as for the production of fuels, the food industry, and waste treatment. More recently, genomic studies of basidiomycete fungi have provided a profound view of the plant-biomass-degrading potential of wood-rotting, litter-decomposing, plant-pathogenic, and ectomycorrhizal (ECM) basidiomycetes. This review summarizes the current knowledge on plant polysaccharide depolymerization by basidiomycete species from diverse habitats. In addition, these data are compared to those for the most broadly studied ascomycete genus, Aspergillus, to provide insight into specific features of basidiomycetes with respect to plant polysaccharide degradation.
Rethinking Disability: Principles for Professional and Social Change

Section 1: FOUNDATIONS. 1. Foundations. 2. Looking Back, Ancient Greece through the 19th Century. 3. Disability in the Twentieth and Twenty-First Centuries. 4. From Bake Sale to Commodity. Section 2: EXPLANATORY LEGITMACY THEORY. 5. The Descriptive Element of Explanatory Legitimacy. 6. Explanations. 7. Legitimacy. 8. Legitimacy from Without. 9. Legitimacy from Within. Section 3: FASHIONING COMMUNITIES. 10. The Traditional Stance: Putting the Cart Before the Horse. 11. Professional Stance Through Explanatory Legitimacy: Putting the Horse Back Where it Belongs. 12. A Social Justice Model of Community Legitimacy. References. Glossary.
Good Epidemiologic Practice in Retinitis Pigmentosa: From Phenotyping to Biobanking

Inherited retinal dystrophies, such as retinitis pigmentosa (RP), include a group of relatively rare hereditary diseases caused by mutations in genes that code for proteins involved in the maintenance and function of the photoreceptor cells (cones and rods). The different forms of RP consist of progressive neurodegenerative disorders which are generally related to various and severe limitations of visual performances. In the course of typical RP (rod-cone dystrophy), the affected individuals first experience night-blindness and/or visual field constriction (secondary to rod dysfunctions), followed by variable alterations of the central vision (due to cone damages). On the other hand, during the atypical form of RP (cone-rod dystrophy), the cone’s functionalities are prevalently disrupted in comparison with the rod’s ones. The basic diagnosis of RP relies upon the documentation of unremitting loss in photoreceptor activity by electroretinogram and/or visual field testing. The prevalence of all RP typologies is variably reported in about one case for each 3000-5000 individuals, with a total of about two millions of affected persons worldwide. The inherited retinal dystrophies are sometimes the epiphenomenon of a complex framework (syndromic RP), but more often they represent an isolated disorder (about 85-90 % of cases). Although 200 causative RP mutations have been hitherto detected in more than 100 different genes, the molecular defect is identifiable in just about the 50% of the analyzed patients with RP. Not only the RP genotypes are very heterogeneous, but also the patients with the same mutation can be affected by different phenotypic manifestations. RP can be inherited as autosomal dominant, autosomal recessive or X-linked trait, and many sporadic forms are diagnosed in patients with no affected relatives. Dissecting the clinico-genetic complexity of RP has become an attainable objective by means of large-scale research projects, in which the collaboration between ophthalmologists, geneticists, and epidemiologists becomes a crucial aspect. In the present review, the main issues regarding clinical phenotyping and epidemiologic criticisms of RP are focused, especially highlighting the importance of both standardization of the diagnostic protocols and appropriateness of the disease’s registration systems.
Two-Photon Absorption, Nonlinear Refraction and Optical Limiting in Semiconductors

Two-photon absorption coefficients /32 of ten direct gap semiconductors with band-gap energy Eg varying between 1 . 4 and 3.7 eV were measured using 1.06 µm and 0.53 um picosecond pulses. $2 was found to scale as E43, as predicted by theory for the samples measured. Extension of the empirical relationship between $2 and Eg to InSb with Eg = 0.2 eV also provides agree-ment between previously measured values and the predicted 02. In addition, the absolute values of $2 are in excellent agreement (the average difference being <26%) with recent theory, which includes the effects of nonparabolic bands. The nonlinear refraction induced in these materials was monitored and found to agree well with the assumption that the self-refraction originates from the two-photon-generated free carriers. The observed self-defocusing yields an effective nonlinear index as much as two orders of magnitude larger than CS2 for comparable irradiances. This self-defocusing, in conjunction with two-photon absorption, was used to construct a simple, effective optical limiter that has high transmission at low input irradiance and low transmission at high input irradiance. The device is the optical analog of a Zener diode.
Title : DNA SEQUENCE VARIATION IN THE PROMOTER REGION OF THE VEGF GENE : IMPACTS ON VEGF GENE EXPRESSION AND MAXIMAL OXYGEN CONSUMPTION

Title: DNA SEQUENCE VARIATION IN THE PROMOTER REGION OF THE VEGF GENE: IMPACTS ON VEGF GENE EXPRESSION AND MAXIMAL OXYGEN CONSUMPTION Steven John Prior, Ph.D., 2005 Directed By: Assistant Professor Stephen M. Roth, Department of Kinesiology Maximal oxygen consumption (Vo2max) is inversely associated with cardiovascular and all-cause mortality and is responsive to aerobic exercise training. A portion of the increase in Vo2max with aerobic exercise training can be attributed to an increase in skeletal muscle capillarity (i.e., angiogenesis), which contributes to increased blood flow and oxygen extraction in working skeletal muscle. One contributing factor to exercise-induced angiogenesis is vascular endothelial growth factor (VEGF), as it is an endothelial cell proliferation and migration factor that is upregulated by acute aerobic exercise. Significant variability has been observed in VEGF protein levels, VEGF gene expression, skeletal muscle capillarity, and Vo2max before and after aerobic exercise training. Additionally, variability is found in the DNA sequence of the gene encoding VEGF. Variation in the VEGF gene has the ability to impact VEGF gene expression and VEGF protein level and because of the relationship between VEGF, angiogenesis, and Vo2max, we hypothesized that variation in the VEGF gene is related to VEGF gene expression in human myoblasts, plasma VEGF level, and Vo2max before and after aerobic exercise training. The present report shows that VEGF promoter region haplotype impacts VEGF gene expression in human myoblasts in vitro. It was also found that VEGF promoter region haplotype was associated with Vo2max in older men and women before and after exercise training in a manner that is consistent with the results of the VEGF gene expression experiments. Additionally, we found that plasma VEGF level was not associated with VEGF promoter region haplotype, nor did plasma VEGF level correlate with baseline Vo2max or ∆Vo2max with aerobic exercise training. To date, we are the first to report that VEGF promoter region haplotype impacts VEGF gene expression in human myoblasts and is associated with Vo2max. These results have potential implications for aerobic exercise training and may also contribute to the understanding of the function of the VEGF promoter region in different cell types. Furthermore, these results may prove relevant in the study of pathological conditions which can be affected by angiogenesis, namely obesity, cancer, coronary artery disease, and peripheral artery disease. DNA SEQUENCE VARIATION IN THE PROMOTER REGION OF THE VEGF GENE: IMPACTS ON VEGF GENE EXPRESSION AND MAXIMAL OXYGEN CONSUMPTION