Miracle-dz/UniFAR-FTUs huggingface dataset:
Two types of zinc fingers are required for dimerization of the serendipity delta transcriptional activator

The serendipity (sry) delta zinc finger protein controls bicoid gene expression during Drosophila melanogaster oogenesis. In addition, sry delta mutants display various zygotic phenotypes, ranging from abnormal embryogenesis to sex-biased adult lethality. We report here that sry delta is a sequence-specific transcriptional activator. A single sry delta consensus binding site (SDCS), in either orientation, is sufficient to promote transcription activation in cell culture, and multiple SDCSs mediate a strong synergistic activation, reflecting the cooperativity of sry delta binding to DNA. Further, several lines of evidence strongly suggest that sry delta binds to DNA as a dimer. While each of three point mutations located in the third zinc finger of sry delta drastically reduces its DNA binding affinity, a fourth mutation, located in the N-terminal region of the protein, specifically affects the cooperativity of DNA binding. This mutation reveals the functional importance of a putative Cys2/Cys2 zinc finger motif of a novel type, located outside the DNA binding domain. A systematic deletion analysis shows that interaction between this proposed Cys2/Cys2 motif and a classical Cys2/His2 zinc finger mediates homodimerization, which is required for DNA binding cooperativity.
Changes in cardiovascular biomarkers in HIV-infected patients switching from ritonavir-boosted protease inhibitors to raltegravir

Background:Switching from boosted protease inhibitors (PI/r) to raltegravir (RAL) results in a better plasma lipid profile than continuing PI/r. Whether this strategy affects plasma biomarkers associated with atherosclerosis is unknown. Methods:We assessed 48-week changes in fasting lipids and several biomarkers including serum high-sensitivity C-reactive protein (hsCRP), monocyte chemoattractant protein 1 (MCP-1), osteoprotegerin, interleukin (IL) 6, IL-10, tumor necrosis factor alpha (TNF-&agr;), intercellular adhesion molecule 1 (ICAM-1), vascular cell adhesion molecule 1 (VCAM-1), E-selectin and P-selectin, adiponectin, insulin, and D-dimer in otherwise healthy, virologically suppressed HIV-infected patients treated with PI/r who randomly switched from PI/r to RAL or continued with PI/r in the SPIRAL trial. Biomarkers and lipids at baseline and 48-week changes between both study arms were compared. Correlations between changes in biomarkers and changes in lipids were also evaluated. Results:Of 273 patients initiating study drugs in the SPIRAL trial, 233 (119 RAL, 114 PI/r) remained on allocated therapy for 48 weeks and had sera available for the purpose of this substudy. Triglycerides (−28%, P < 0.0001), total (−14%, P < 0.0001), low-density lipoprotein (−9%, P = 0.0069), and high-density lipoprotein (−10%, P = 0.0017) cholesterol decreased in RAL relative to the PI/r group. Among biomarkers, hsCRP (−40%, P < 0.0001), MCP-1 (−20%, P = 0.0003), osteoprotegerin (−13%, P = 0.0024), IL-6 (−46%,P < 0.0001), TNF-&agr; (−27%, P = 0.0011), insulin (−26%, P < 0.0001), and D-dimer (−8%, P = 0.0187) decreased in RAL relative to PI/r group, whereas IL-10 (+1%, P = 0.7773), ICAM-1 (−6%, P = 0.1255), VCAM-1(0%, P = 0.8671), E-selectin (−9%, P = 0.2174), P-selectin (−6%, P = 0.3865), and adiponectin (+8%, P = 0.2028) remained unchanged. Biomarkers and lipids changes at 48 weeks were weakly correlated. Conclusion:Switching from PI/r to RAL induced significant changes in several cardiovascular biomarkers that were not completely explained by lipid changes.
Continuous Psoas Compartment Block for Anesthesia and Perioperative Analgesia in Patients With Hip Fractures

Background and Objectives. The perioperative use of continuous psoas compartment block (CPCB) was compared with traditional pain management for patients with fracture of the femur. The anatomy of CPCB was also tested in cadavers. Methods. Forty consecutive patients (range, 67-96 years old) were prospectively randomized either to group A (given local anesthetics using a CPCB) or group B (given perioperative analgesia with meperidine). In another part of the study, CPCB was performed in 15 fresh cadavers, and dissection of the lumbar region was performed after dye injection. Results. Continuous psoas compartment block was performed successfully in all patients in group A and was used in the pre- (16-48 hours) and postoperative (72 hours) periods. Visual analog scale score in group A was lower than in group B in 5/7 preoperative and 9/9 postoperative 8 hourly assessments. Differences reached statistical significance (P < .05) in 3 and 5 of the assessments, respectively. Patient satisfaction was higher in group A in the pre- (P < .05) and postoperative periods (P < .03). The block failed to achieve surgical anesthesia in 85% (17/20) of the patients, and additional anesthesia was needed. The anatomic study failed to support the existence of a defined “psoas compartment” previously described, and supported the clinical findings. Injected dye was found in the region of the origin of the sciatic nerve (essential for the production of anesthesia for hip surgery) in only 26% (4/15) of cadavers. Conclusions. The CPCB seems to be an appropriate technique for efficient and safe perioperative pain control. However, in our dissections, the psoas compartment was not well defined in all patients, thus, using this route for anesthesia may result in only partial success.
Modal Series Expansion of Eigensolutions for Closed and Open Periodic Waveguides

An efficient approach is presented to compute the eigensolutions of closed and open radiating periodically loaded waveguides by modal series expansion. The eigensolutions of the homogeneous background waveguides serve as basis functions for the fields in the periodic boundaries. The corresponding scattering matrix of an isolated periodic unit cell is determined by commercial software solvers. The scattering matrix is transformed into the transfer matrix, which can be used to formulate an eigenproblem. Open field problems are converted into a closed equivalence while the characteristics of the original open configurations are preserved, even for radiating (leaky) waveguiding structures. Consequently, the original continuous spectrum of modes is represented by a discrete and proper set of modes. An eigenproblem must still be solved but it is considerably reduced in size and complexity for configurations where relatively few expansion modes are sufficient.
Phishing detection: A recent intelligent machine learning comparison based on models content and features

In the last decade, numerous fake websites have been developed on the World Wide Web to mimic trusted websites, with the aim of stealing financial assets from users and organizations. This form of online attack is called phishing, and it has cost the online community and the various stakeholders hundreds of million Dollars. Therefore, effective counter measures that can accurately detect phishing are needed. Machine learning (ML) is a popular tool for data analysis and recently has shown promising results in combating phishing when contrasted with classic anti-phishing approaches, including awareness workshops, visualization and legal solutions. This article investigates ML techniques applicability to detect phishing attacks and describes their pros and cons. In particular, different types of ML techniques have been investigated to reveal the suitable options that can serve as anti-phishing tools. More importantly, we experimentally compare large numbers of ML techniques on real phishing datasets and with respect to different metrics. The purpose of the comparison is to reveal the advantages and disadvantages of ML predictive models and to show their actual performance when it comes to phishing attacks. The experimental results show that Covering approach models are more appropriate as anti-phishing solutions, especially for novice users, because of their simple yet effective knowledge bases in addition to their good phishing detection rate.
TESTING THE DI'FFERENCES BETWEEN THE DETERMINANTS OF MOODY'S AND STANDARD & POOR'S RATINGS

SUMMARY This paper extends previous studies on bond ratings by modeling as a system of equations the determinants of a municipality's decision to obtain a bond rating and the determinants of the municipality's rating for the two major rating agencies. Our model provides a framework to examine formally the differences between the two agencies in the determinants of the ratings. We estimate the four-equation system by smooth simulated maximum likelihood estimation and then construct minimum X2 tests on cross-equation restrictions based on optimal minimum distance estimation. Self-selection is found to be important in Moody's ratings while not in those of S&P. Split ratings appear to reflect differences in both the weight attached to specific determinants of the ratings and differences in the way the bonds are classified.
In Vitro Functional Gut‐Like Organ Formation from Mouse Embryonic Stem Cells

Background and Aims. Embryonic stem (ES) cells have a pluripotent ability to differentiate into a variety of cell lineages in vitro. We have recently found that ES cells can give rise to a functional gut‐like unit, which forms a three‐dimensional dome‐like structure with lumen and exhibits mechanical activity, such as spontaneous contraction and peristalsis. The aim of the present study was to investigate the electrophysiological and morphological properties of ES cell‐derived contracting clusters.
Sustaining the future of HIV counselling to reach 90-90-90: a regional country analysis

Counselling services are recommended by the World Health Organization and have been partially adopted by national HIV guidelines. In settings with a high HIV burden, patient education and counselling is often performed by lay workers, mainly supported with international funding. There are few examples where ministries of health have been able to absorb lay counsellors into their health systems or otherwise sustain their work. We document the role of lay cadres involved in HIV testing and counselling and adherence support and discuss approaches to sustainability.
A Case Report of Mycobacterium Abscessus Peritonitis in a Peritoneal Dialysis Patient

Abstract: Peritonitis due to nontuberculous mycobacterium in peritoneal dialysis (PD) patients is rare. However, when it occurs, PD catheter removal is required in most cases because of resistance to antibiotic therapy. We report a case of Mycobacterium abscessus peritonitis subsequent to tunnel infection after PD catheter‐replacement surgery. The patient underwent this surgery as her tunnel infection had not resolved following the usual 3 month course of antibiotic therapy. After surgery, tunnel infection of the second catheter and peritonitis occurred. Nontuberculous mycobacteria were detected on acid‐fast stain from both the old and new exit‐site drainage and the peritoneal effluent. The mycobacteria were identified as M. abscessus. Removal of the new catheter and surgical excision of the previous catheter tunnel were performed and multiple antibiotics were started. After 3 months the postsurgical wounds had healed completely. This case demonstrates the importance of further evaluation of unidentified PD catheter‐related infections, including an examination for nontuberculous mycobacterium.
αCP Poly(C) Binding Proteins Act as Global Regulators of Alternative Polyadenylation

ABSTRACT We have previously demonstrated that the KH-domain protein αCP binds to a 3′ untranslated region (3′UTR) C-rich motif of the nascent human alpha-globin (hα-globin) transcript and enhances the efficiency of 3′ processing. Here we assess the genome-wide impact of αCP RNA-protein (RNP) complexes on 3′ processing with a specific focus on its role in alternative polyadenylation (APA) site utilization. The major isoforms of αCP were acutely depleted from a human hematopoietic cell line, and the impact on mRNA representation and poly(A) site utilization was determined by direct RNA sequencing (DRS). Bioinformatic analysis revealed 357 significant alterations in poly(A) site utilization that could be specifically linked to the αCP depletion. These APA events correlated strongly with the presence of C-rich sequences in close proximity to the impacted poly(A) addition sites. The most significant linkage was the presence of a C-rich motif within a window 30 to 40 bases 5′ to poly(A) signals (AAUAAA) that were repressed upon αCP depletion. This linkage is consistent with a general role for αCPs as enhancers of 3′ processing. These findings predict a role for αCPs in posttranscriptional control pathways that can alter the coding potential and/or levels of expression of subsets of mRNAs in the mammalian transcriptome.
Endpoints After Empire: Explaining Varying Levels of Democracy in Post-Communist Europe

DIFFERENT ENDPOINTS AFTER EMPIRE: EXPLAINING VARYING LEVELS OF DEMOCRACY IN POST-COMMUNIST EASTERN EUROPE William John Eger, Jr. Old Dominion University, 2017 Director: Dr. Simon Serfaty The varying levels of democracy in central and eastern Europe provide scholars with an interesting study of democratization. Democracy grew to different levels and in varying ways in the region since the collapse of communism. The evolution of democracy in the region offers insight into which variables affect democracy, a test for established theories of democracy, and a workshop for new theories and hypotheses addressing democratization. This study sought to determine the impetus behind varying levels of post-communist democratization in the states of the region. It explores the different theories of democratization. The work takes a regional approach to examining the states. This approach isolates less traditional factors that contribute to democratic quality: history, culture and geography. Each of the factors is relevant to democracy in the region. The exploration of the historical background explains some of the forces still at work in the region. It presents the core causes of some of the democratic short-comings that exist. It also assists in a presentation of the next contextual factor: how the political parties and systems evolved since 1989. Religion in the region is especially relevant to the degree of rights and freedoms, as well. The area is very diverse, with some countries of predominantly Catholic, some states with sizeable Islamic segments, countries with overwhelming Eastern Orthodox majorities and states with a relevant number of Protestant Christians. Finally, the region‟s location has a bearing of democracy. The region represents the eastern border of western civilization. Not only does this account for their religious diversity in many areas and ethnic diversity in others, it also helps define some of the aspects of their democracy. The region long found itself as the battlefields of wars between those of the west and those of the east. The predicament of being trapped between two giants continues
Identification and characterization of a novel heparin‐binding peptide for promoting osteoblast adhesion and proliferation by screening an Escherichia coli cell surface display peptide library

Heparin/heparan sulfate (HS) plays a key role in cellular adhesion. In this study, we utilized a 12‐mer random Escherichia coli cell surface display library to identify the sequence, which binds to heparin. Isolated insert analysis revealed a novel heparin‐binding peptide sequence, VRRSKHGARKDR, designated as HBP12. Our analysis of the sequence alignment of heparin‐binding motifs known as the Cardin–Weintraub consensus (BBXB, where B is a basic residue) indicates that the HBP12 peptide sequence contains two consecutive heparin‐binding motifs (i.e. RRSK and RKDR). SPR‐based BIAcore technology demonstrated that the HBP12 peptide binds to heparin with high affinity (KD = 191 nM). The HBP12 peptide is found to bind the cell surface HS expressed by osteoblastic MC3T3 cells and promote HS‐dependent cell adhesion. Moreover, the surface‐immobilized HBP12 peptide on titanium substrates shows significant increases in the osteoblastic MC3T3‐E1 cell adhesion and proliferation. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
Rapid magnetic resonance imaging vs radiographs for patients with low back pain: a randomized controlled trial.

CONTEXT Faster magnetic resonance imaging (MRI) scanning has made MRI a potential cost-effective replacement for radiographs for patients with low back pain. However, whether rapid MRI scanning results in better patient outcomes than radiographic evaluation or a cost-effective alternative is unknown. OBJECTIVE To determine the clinical and economic consequences of replacing spine radiographs with rapid MRI for primary care patients. DESIGN, SETTING, AND PATIENTS Randomized controlled trial of 380 patients aged 18 years or older whose primary physicians had ordered that their low back pain be evaluated by radiographs. The patients were recruited between November 1998 and June 2000 from 1 of 4 imaging centers in the Seattle, Wash, area: a university-based teaching program, a nonuniversity-based teaching program, and 2 private clinics. INTERVENTION Patients were randomly assigned to receive lumbar spine evaluation by rapid MRI or by radiograph. MAIN OUTCOME MEASURES Back-related disability measured by the modified Roland questionnaire. Secondary outcomes included Medical Outcomes Study 36-Item Short Form Health Survey (SF-36), pain, preference scores, satisfaction, and costs. RESULTS At 12 months, primary outcomes of functional disability were obtained from 337 (89%) of the 380 patients enrolled. The mean back-related disability modified Roland score for the 170 patients assigned to the radiograph evaluation group was 8.75 vs 9.34 for the 167 patients assigned the rapid MRI evaluation group (mean difference, -0.59; 95% CI, -1.69 to 0.87). The mean differences in the secondary outcomes were not statistically significant : pain bothersomeness (0.07; 95% CI -0.88 to 1.22), pain frequency (0.12; 95% CI, -0.69 to 1.37), and SF-36 subscales of bodily pain (1.25; 95% CI, -4.46 to 4.96), and physical functioning (2.73, 95% CI -4.09 to 6.22). Ten patients in the rapid MRI group vs 4 in the radiograph group had lumbar spine operations (risk difference, 0.34; 95% CI, -0.06 to 0.73). The rapid MRI strategy had a mean cost of 2380 dollars vs 2059 dollars for the radiograph strategy (mean difference, 321 dollars; 95% CI, -1100 to 458). CONCLUSIONS Rapid MRIs and radiographs resulted in nearly identical outcomes for primary care patients with low back pain. Although physicians and patients preferred the rapid MRI, substituting rapid MRI for radiographic evaluations in the primary care setting may offer little additional benefit to patients, and it may increase the costs of care because of the increased number of spine operations that patients are likely to undergo.
Localizing Age-Related Changes in Brain Structure between Childhood and Adolescence Using Statistical Parametric Mapping

Volumetric studies have consistently shown reductions in cerebral gray matter volume between childhood and adolescence, with the most dramatic changes occurring in the more dorsal cortices of the frontal and parietal lobes. The purpose of this study was to examine the spatial location of these changes employing methods typical of functional imaging studies. T1-weighted structural MRI data (1.2 mm) were analyzed for nine normally developing children and nine normal adolescents. Validity and reliability of the tissue segmentation protocol were assessed as part of several preprocessing analyses prior to statistical parametric mapping (SPM). Using SPM96, a simple contrast of average gray matter differences between the two age groups revealed 57 significant clusters (SPM[Z] height threshold, P<0.001, extent threshold 50, uncorrected). The pattern and distribution of differences were consistent with earlier findings from the volumetric assessment of the same subjects. Specifically, more differences were observed in dorsal frontal and parietal regions with relatively few differences observed in cortices of the temporal and occipital lobes. Permutation tests were conducted to assess the overall significance of the gray matter differences and validity of the parametric maps. Twenty SPMs were created with subjects randomly assigned to groups. None of the random SPMs approached the number of significant clusters observed in the age difference SPM (mean number of significant clusters = 5.8). The age effects observed appear to result from regions that consistently segment as gray matter in the younger group and consistently segment as white matter in the older group. The utility of these methods for localizing relatively subtle structural changes that occur between childhood and adolescence has not previously been examined.
Characterizing the Nature of Visual Conscious Access: The Distinction between Features and Locations

The difference between the roles of features and locations has been a central topic in the theoretical debates on visual attention. A recent theory proposed that momentary visual awareness is limited to one Boolean map, that is the linkage of one feature per dimension with a set of locations (Huang & Pashler, 2007). This theory predicts that: (a) access to the features of a set of objects is inefficient whereas access to their locations is efficient; (b) shuffling the locations of objects disrupts access to their features whereas shuffling the features of objects has little impact on access to their locations. Both of these predictions were confirmed in Experiments 1 and 2. Experiments 3 and 4 showed that this feature-location distinction remains when the task involves the detection of changes to old objects rather than the coding of new objects. Experiments 5 and 6 showed that, in a prespecified set, one missing location can be readily detected, but detecting one missing color is difficult. Taken together, multiple locations seem to be accessed and represented together as a holistic pattern, but features have to be handled as separate labels, one at a time, and do not constitute a pattern in featural space.
The Effect of Heterogeneous Wage Contracts on Macroeconomic Volatility in a Financially Fragile Economy

I build a small open economy (SOE) dynamic stochastic general equilibrium (DSGE) model to investigate the effect of a heterogeneous wage contract between regular and temporary workers on a macroeconomic volatility in a financially fragile economy. The imperfect financial market condition is captured by a quadratic financial adjustment cost for borrowing foreign assets, and the labor market friction is captured by a Nash bargaining process which is only available to the regular workers when they negotiate their wages with the firms while the temporary workers are given their wage which simply equals the marginal cost. As a result of impulse responses to a domestic productivity shock, the higher elasticity of substitution between two types of workers and the lower weight on the regular workers in the firm’s production process induce the higher volatilities in most variables. This is reasoned that the higher substitutability creates more volatile wage determination process while the lower share of the regular workers weakens their Nash bargaining power in the contract process.