Miracle-dz/UniFAR-FTUs huggingface dataset:
Leveling the Playing Field in Homozygosity Mapping Using Map Distances

Studies of linkage disequilibrium (LD) and its variation in the genome are of central importance for understanding evolutionary history, population structure, and selective sweeps. Extreme forms of the latter may result in runs of homozygosity (ROH). In human gene mapping, long ROHs are the basis for homozygosity mapping (HM) with length measured in terms of Mb (106 base pairs physical distance). LD varies greatly over the human genome so that long ROHs tend to occur preferentially in regions of high LD and ROHs of the same length in different regions are not strictly comparable. Thus, in human gene mapping, LD appears as a confounder that needs to be taken into account in the interpretation of ROHs. The effect of varying LD can be mitigated by working on a scale of centimorgans (cM, genetic distance) instead of Mb. We demonstrate this effect for HapMap 3 data on chromosome 19 and show examples with different ROH lengths depending on whether physical or genetic lengths are used. These results suggest that HM should preferably be done on genetic rather than physical distances.
The meaning of family routines in a homeless shelter.

OBJECTIVE This exploratory investigation sought to understand what meaning parents, living in a homeless shelter, attribute to family routines and the nature of those routines. METHOD In-depth interviews were conducted with 12 parents living in a homeless shelter. Thematic analysis was employed to develop descriptive codes and themes from transcribed data and field notes. RESULTS Parents described family routines focused on three features: promoting intimacy, maintaining or developing a legacy, and connections with the community. These routines seemed to preserve family integrity while homeless and to provide hope for the family to continue into the future. CONCLUSIONS Homeless parents, in this investigation, seemed to expend a substantial amount of energy to create or maintain family routines while living in a homeless shelter. Findings suggest that occupational therapy services may help support homeless parents as they exercise their role as the organizer of family routines.
1 Report on Shape Analysis and Matching and on Semantic Matching 2016-03-16

that have been already implemented in cultural heritage or we think are useful for the GRAVITATE project. These fields are relatively disjoint, and the research and development challenge of GRAVITATE is precisely to merge them. After the review of the current literature on these fields, we end the report with common remarks on possible or plausible crossconnections that suggest themselves. These considerations will be refined for the Roadmap for Research deliverable. D3.1
Scanning Approaches of 2-D Resistive Sensor Arrays: A Review

With scanning approaches of low complexity, the 2-D resistive sensor arrays (RSAs) are used to extract the distribution of sensed variable values (e.g., physical pressure) over the sensing area. This review surveys the scanning approaches of the 2-D RSAs, their evaluation methods, and their applications. The principle of the 2-D RSA with the scanning approach is introduced first. Then, different scanning approaches of RSAs are illustrated. The scanning approaches of RSAs are mainly categorized into the inserting diode method, the inserting transistor method, the passive integrator method, the resistance matrix approach, the incidence matrix approach, the voltage feedback method, the zero potential method, and so on. Next, various evaluation methods of the scanning approaches are presented. The scanning approach’s evaluation methods are categorized into testing of the actual system, analyzing with circuit simulation software, and analyzing with test model. Followed, typical applications of the 2-D RSAs with the scanning approaches and their special requirements are analyzed. Finally, the characteristics of various typical scanning approaches and their development tendency are discussed and investigated in detail.
Privatizing water: governance failure and the world's urban water crisis

Stern’s larger trilogy will long be remembered as a tour de force. It is the most sophisticated historical account of Pinochet’s Chile and a creative exploration into the role of memory in human rights struggles. Scholars working on issues of human rights truth-telling and accountability, in any region of the world, will benefit from Stern’s complex conceptualization of memory. Students of democratization would do well to follow Stern’s lead in moving beyond a popular focus on “pacted” transitions, often featuring Chile, to explore the broader social context shaping political bargains. The range of source materials, along with the author’s eye for socio-cultural detail, further exemplify how conceptually rich historical work can advance our understanding of human rights issues. When members of a society reckon with past human rights abuses, the answers can never be clear or simple. These people were participants in the reality they are contesting, just as they must overcome the past to build a future together. How to capture this “reality of the impossible”9 in words and images is our central challenge as observers. In Reckoning with Pinochet, Stern shows us admirably how to represent, and somehow make sense of, memories of human rights atrocity.
Vascular endothelial growth factor induces EDRF-dependent relaxation in coronary arteries.

Vascular endothelial growth factor (VEGF), also known as vascular permeability factor (VPF), has recently been shown to increase cytosolic free calcium in endothelial cells. In the present study, we investigated the coronary vascular effects of recombinant human and native guinea pig VEGF/VPF in isolated canine coronary arteries in the presence and absence of intimal endothelium, indomethacin, and NG-monomethyl-L-arginine, a competitive nitric oxide synthase inhibitor. Addition of recombinant VEGF/VPF (1-660 pM) in coronary arteries that had been previously contracted with prostaglandin F2 alpha induced a slow, dose-dependent relaxation, reaching a maximum of -59.1 +/- 6.7% (mean +/- SE, n = 19). Mechanical disruption of the intimal endothelium completely abolished the observed relaxation. No direct vascular effect of recombinant VEGF/VPF on the endothelium-disrupted coronary arteries was noted. Pretreatment of endothelium-intact coronary arteries with 5 microM of indomethacin did not alter the observed relaxation (-57.3 +/- 7.0%, n = 18), whereas pretreatment with either NG-monomethyl-L-arginine or 10 microM of genistein, a known inhibitor of tyrosine kinase, significantly inhibited the relaxation. Addition of native VEGF/VPF (1-100 pM) also induced an endothelium-dependent relaxation in the isolated coronary arteries. Heating of recombinant VEGF/VPF (70 degrees C, 25 min) or prior incubation with a specific antibody raised against a VEGF/VPF peptide completely abolished the relaxation. Finally, recombinant VEGF/VPF stimulated a slow rise in cytosolic free calcium in cultured human endothelial cells that was qualitatively similar to that of native VEGF/VPF. (ABSTRACT TRUNCATED AT 250 WORDS)
Convergence and Stability in US Regional Employment

It is widely believed that regional labour markets in the USA are highly flexible, so that employment shocks have only transitory effects on joblessness since induced migration quickly offsets much of the initial impact. However time-series analysis of the response to shocks is very sensitive to errors of measurement in labour market data, and such errors are large in some widely used series which depend on household surveys of limited size. Adjusting for the likelihood magnitude of such errors with some novel statistical approaches, and using a range of data sources, we show that the responsiveness of employment rates to shocks has been rather weak in the USA over the past 30 years, though probably stronger in the 1950s and 1960s. This suggests that flexible regional adjustment is not a major factor behind the contemporary success of monetary union in the USA.
Noninvasive, Accurate Assessment of the Behavior of Representative Populations of Motor Units in Targeted Reinnervated Muscles

Targeted muscle reinnervation (TMR) redirects nerves that have lost their target, due to amputation, to remaining muscles in the region of the stump with the intent of establishing intuitive myosignals to control a complex prosthetic device. In order to directly recover the neural code underlying an attempted limb movement, in this paper, we present the decomposition of high-density surface electromyographic (EMG) signals detected from three TMR patients into the individual motor unit spike trains. The aim was to prove, for the first time, the feasibility of decoding the neural drive that would reach muscles of the missing limb in TMR patients, to show the accuracy of the decoding, and to demonstrate the representativeness of the pool of extracted motor units. Six to seven flexible EMG electrode grids of 64 electrodes each were mounted over the reinnervated muscles of each patient, resulting in up to 448 EMG signals. The subjects were asked to attempt elbow extension and flexion, hand open and close, wrist extension and flexion, wrist pronation and supination, of their missing limb. The EMG signals were decomposed using the Convolution Kernel Compensation technique and the decomposition accuracy was evaluated with a signal-based index of accuracy, called pulse-to-noise ratio (PNR). The results showed that the spike trains of 3 to 27 motor units could be identified for each task, with a sensitivity of the decomposition >90%, as revealed by PNR. The motor unit discharge rates were within physiological values of normally innervated muscles. Moreover, the detected motor units showed a high degree of common drive so that the set of extracted units per task was representative of the behavior of the population of active units. The results open a path for a new generation of human-machine interfaces in which the control signals are extracted from noninvasive recordings and the obtained neural information is based directly on the spike trains of motor neurons.
X-ray- and neutron-scattering studies of alpha-crystallin and evidence that the target protein sits in the fenestrations of the alpha-crystallin shell.

PURPOSE Alpha-crystallin, a ubiquitous molecular chaperone, is found in high concentrations in the lens. Its structure and precise mechanism of action, however, are unknown. The purpose of these experiments was to further the understanding of the chaperone function of alpha-crystallin. METHODS X-ray- and neutron-solution-scattering studies were used to measure the radius of gyration of bovine lens alpha-crystallin when complexed with its target protein beta-crystallin in both normal and heavy-water-based solutions. Spectrophotometry was used as a chaperone assay. RESULTS The radius of gyration of alpha-crystallin on its own and when mixed with beta-crystallin was 69 +/- 1 A at 35 degrees C and increased with the temperature. In contrast to H2O-buffered solutions, the radius of gyration did not increase significantly in D2O-buffered solutions up to 55 degrees C, and at 70 degrees C was, on average, some 15 to 20 A smaller. CONCLUSIONS Bovine lens alpha-crystallin in solution can be modeled as a fenestrated spherical shell of diameter 169 A. At physiological temperatures, a weak interaction between alpha- and beta-crystallin occurs, and beta-crystallin is located in the fenestrations. Deuterium substitution indicates that the superaggregation process is controlled by hydrogen bonding. However, the chaperone process and superaggregation appear not to be linked.
Structural Basis for Amplifying Vinculin Activation by Talin*

Talin interactions with vinculin are essential for focal adhesions. Curiously, talin contains three noncontiguous vinculin binding sites (VBS) that can bind individually to the vinculin head (Vh) domain. Here we report the crystal structure of the human Vh·VBS1 complex, a validated model of the Vh·VBS2 structure, and biochemical studies that demonstrate that all of talin VBSs activate vinculin by provoking helical bundle conversion of the Vh domain, which displaces the vinculin tail (Vt) domain. Thus, helical bundle conversion is a structurally conserved response in talin-vinculin interactions. Furthermore, talin VBSs bind to Vh in a mutually exclusive manner but do differ in their affinity for Vh and in their ability to displace Vt, suggesting that the strengths of these interactions could lead to differences in signaling outcome. These findings support a model in which talin binds to and activates multiple vinculin molecules to provoke rapid reorganization of the actin cytoskeleton.
Dolar/Euro Paritesinin Türkiye’nin İhracatına Etkisi: Ekonometrik Bir Analiz.

Turkey performs its exports mostly based on Euros whereas its imports on US dollar. In addition, most of its imports is raw materials while the share of the consumer products is visibly higher in the exports. This makes Turkey a country that uses the imported raw materials in US currency and exports the final products on Euro. This structure in foreign trade points to the real impact of the changes in the dollar/euro parity in Turkey's exports. The valuation of euros against the dollar may promote exports by reducing the costs via imported inputs. The devaluation of the euros against dollar should have a discouraging impact on the exports by increasing the input costs. This study analyzes whether the changes in the euro/dollar parity have actually impacted upon Turkey's exports by focusing on three-month periods between 2002 and 2010. The study concludes that the changes in euro/dollar parity affect Turkey's real exports in both long and short terms. This impact is strong in short term and less visible in long run.
Biophysical properties of Kv3.1 channels in SH-SY5Y human neuroblastoma cells.

Biophysical properties of delayed rectifier K channels in the human neuroblastoma SH-SY5Y were established using patch clamp recordings. The whole cell K+ conductance activated at membrane potentials positive to -20 mV. The midpoint of current activation was 9.6 +/- 5.1 mV, the equivalent charge was 3.7 +/-. 6. Whole-cell currents inactivated slightly with time constants of 700 ms and 5 s. The K+ currents were sensitive to micromolar concentrations of TEA and 4-aminopyridine. RT-PCR experiments amplified a cDNA fragment specific for human Kv3.1 channels. Activation gating parameters in outside-out patches were shifted by approximately 14 mV in the hyperpolarizing direction.
Inhibition of EHMT2/G9a epigenetically increases the transcription of Beclin-1 via an increase in ROS and activation of NF-κB

We previously reported that BIX-01294 (BIX), a small molecular inhibitor of euchromatic histone-lysine N-methyltransferase 2 (EHMT2/G9a), induces reactive oxygen species (ROS)-dependent autophagy in MCF-7 cells. Herein, we analyzed the epigenetic mechanism that regulates the transcription of Beclin-1, a tumor suppressor and an autophagy-related gene (ATG). Inhibition of EHMT2 reduced dimethylation of lysine 9 on histone H3 (H3K9me2) and dissociated EHMT2 and H3K9me2 from the promoter of Beclin-1. To this promoter, RNA polymerase II and nuclear factor kappa B (NF-κB) were recruited in a ROS-dependent manner, resulting in transcriptional activation. Moreover, treatment with BIX reversed the suppression of Beclin-1 by the cooperative action of EHMT2 and DNA methyltransferase 1 (DNMT1). Accordingly, a combination treatment with BIX and 5-Aza-2′-deoxycytidine (5-Aza-Cd), a DNMT1 inhibitor, exerted a synergistic effect on Beclin-1 expression. Importantly, high levels of EHMT2 expression showed a significant association with low levels of Beclin-1 expression, which was related to a poor prognosis. These findings suggest that EHMT2 can directly repress Beclin-1 and that the inhibition of EHMT2 may be a useful therapeutic approach for cancer prevention by activating autophagy.
The Prevalence and Characteristics of Psoriatic Arthritis in Patients With Psoriasis in a Tertiary Hospital

Objectives: This study aims to investigate psoriatic arthritis (PsA) prevalence in patients with psoriasis (Ps), and compare clinical and laboratory characteristics of patients with or without PsA. Patients and methods: A total of 126 patients (59 males, 67 females; mean age 45.6±13.8 years; range 18 to 82 years) with Ps who applied to Dermatology Outpatient Clinic between October 2009 and September 2010 were included in this study. The patients were screened for PsA using Classification of Psoriatic Arthritis criteria. The patients classified as PsA were grouped according to Moll and Wright criteria. Enthesopathy was evaluated according to Maastricht Ankylosing Spondylitis Enthesis score. Psoriasis Area and Severity Index scores were calculated by the same dermatologist. Results: The prevalence of PsA was 25.4%. Ps duration was significantly longer in the group with PsA. The most common type was asymmetrical oligoarticular type (53.1%). Compared to previous studies, the rate of isolated spondyloarthropahty was higher in our study (21.9%). Nail involvement, Psoriasis Area and Severity Index score, mean erythrocyte sedimentation rate, and C-reactive protein values were significantly higher in the group with PsA. Conclusion: High rate of isolated spondyloarthropahty in patients with PsA indicates that PsA must be kept in mind in the differential diagnosis of seronegative spondyloarthropathies. The fact that nail involvement is seen more frequently in patients with arthritis may assist in screening of PsA in patients with Ps. In addition, our results showing a higher probability of PsA development in patients with more severe skin lesions and a higher probability of arthritis development in patients with long lasting Ps may guide clinicians in terms of the probability of arthritis development in patients with Ps.
VR closure rates for two vocational models.

BACKGROUND The Individual Placement and Support (IPS) model of supported employment is an evidence-based practice for individuals with psychiatric disabilities. To be financially viable, IPS programs require funding from the state-federal vocational rehabilitation (VR) system. However, some observers have questioned the compatibility of IPS and the VR system. METHOD Using a randomized controlled trial comparing IPS to a well-established vocational program called the Diversified Placement Approach (DPA), we examined rates of VR sponsorship and successful VR closures. We also describe the establishment of an active collaboration between a psychiatric rehabilitation agency and the state VR system to facilitate rapid VR sponsorship for IPS clients. FINDINGS Both IPS and DPA achieved a 44% rate of VR Status 26 closure when considering all clients entering the study. IPS and DPA averaged similar amount of time to achieve VR sponsorship. Time from vocational program entry to Status 26 was 51 days longer on average for IPS. CONCLUSIONS Even though several IPS principles seem to run counter to VR practices, such as zero exclusion and rapid job search, we found IPS closure rates comparable to those for DPA, a vocational model that screens for readiness, provides prevocational preparation, and extensively uses agency-run businesses.
Differences in acute alcohol-induced behavioral responses among zebrafish populations.

BACKGROUND With the arsenal of genetic tools available for zebrafish, this species has been successfully used to investigate the genetic aspects of human diseases from developmental disorders to cancer. Interest in the behavior and brain function of zebrafish is also increasing as CNS disorders may be modeled and studied with this species. Alcoholism and alcohol abuse are among the most devastating and costliest diseases. However, the mechanisms of these diseases are not fully understood. Zebrafish has been proposed as a model organism to study such mechanisms. Characterization of alcohol's effects on zebrafish is a necessary step in this research. METHODS Here, we compare the effects of acute alcohol (EtOH) administration on the behavior of zebrafish from 4 distinct laboratory-bred populations using automated as well as observation based behavioral quantification methods. RESULTS Alcohol treatment resulted in significant dose-dependent behavioral changes but the dose-response trajectories differed among zebrafish populations. CONCLUSIONS The results demonstrate for the first time a genetic component in alcohol responses in adult zebrafish and also show the feasibility of high throughput behavioral screening. We discuss the exploration and exploitation of the genetic differences found.
4Gbit density STT-MRAM using perpendicular MTJ realized with compact cell structure

For the first time, 4Gbit density STT-MRAM using perpendicular MTJ in compact cell was successfully demonstrated through the tight distributions for resistance and magnetic properties. This paper includes the results regarding parasitic resistance control process, MTJ process, and MTJ stack engineering. Both of successful 4Gb read and write operations were performed with high TMR, low Ic. This result will brighten the prospect of high-density STT-MRAM.
Middle East Studies After 9/11: An Exit from Arab Autocracy

In the aftermath of September 11, Arab politics have come under unprecedented scrutiny in the West. As the unremittingly authoritarian nature of Arab regimes has come into ever sharper focus, this lack of democracy is decried as a cause of anti-regime and anti-Western violence at the same time that it is depicted as the only reliable short-term shield against the exact same phenomena. Arab autocracies, it is argued, encourage violence domestically by blocking peaceful change, and export violence by using state-controlled media to deflect demands for accountability with propaganda against the United States, Jews, or the West. These same autocracies, however, must be supported because they are all that blocks the rise to power of even more viciously authoritarian and illiberal groups. Since the Arab world lacks popular ultranationalist movements, the most likely candidates for the category of illiberal challengers are Islamist parties, whose presumed commitment to Islamic law (shari’a) renders them debatable defenders of democracy at best. Scholars unwilling to write the Arab world off as congenitally inhospitable to democracy generally advocate one of two gradual paths for the exit from autocracy. Both start from the same assumption—that if free elections were held today, Islamist parties would win, either because many Arab voters support them or because opponents would be inadequately mobilized to defeat them. The first proposed exit from this situation is an economic one—delay meaningful democratization until economic development creates middle classes, widely thought to foster liberal democracy and hinder extremism. The second approach focuses Vickie Langohr is assistant professor of political science at the College of the Holy Cross in Worcester, Massachusetts. She has published essays in the on-line version of the Middle East Report as well as in the International Journal of Middle East Studies, and is currently working on a book about religious nationalist movements in the Middle East and South Asia.
Power in the union?: Part‐time workers and enterprise unionism in Japan

Increases in the number of jobs for part‐time workers has had little impact on the rate of unionisation for part‐time workers, the majority of whom are women. The argument run by union officials in Japan is that women, and thus part‐time workers, are not interested in industrial issues. This study explores an alternative explanation which is that union officials and “core” male workers are excluding women and part‐time workers in order to protect their own privileged position. Whilst it is acknowledged that the organisational structure of enterprise unions makes it difficult to incorporate the needs of part‐time workers, it is the attitudes of “core” male workers and union officials to women as paid workers that is the major hurdle to the non‐unionisation of part‐time workers. For women and part‐time workers there is no power in the union.