Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of a new k-means approach for exploratory clustering of items

For the exploratory analysis of survey data commonly the exploratory factor analysis (EFA) is used. However, EFA is known to exhibit some problems. The major mathematical issue is the factor indeterminacy. Further problems are for example its weak performance in small sample sizes (n ≤ 150) and with high cross-loadings (e.g. Guadagnoli & Velicer, 1988; Sass, 2010; Wayne F. Velicer & Fava, 1998) as well as the general issue of the underlying measurement model including uncorrelated residual variances, what may be difficult to justify (Cudeck & Henly, 1991; MacCallum & Tucker, 1991; R. C. Tryon, 1959). The authors suggest two new k-means approaches as an alternative: k-means scaled distance measure (sdm) where items are represented in a coordinate system in a way so that their distance is based on one minus their correlation; and k-means cor where item inter-correlations are directly taken as the coordinate points of the items. These approaches were tested in a resampling with two real data sets and a traditional Monte Carlo simulation, as well as in a cross validation using confirmatory factor analysis (CFA). For dimensionality assessment the cluster validity coefficient Silhouette was used. In either analysis these approaches were compared to existing cluster analysis approaches and EFA. The authors conclude that the main advantage of the new approaches are (a) that cluster scores are determinate and (b) for item assignment kmeans sdm obtains better results than EFA and other cluster analysis approaches. The authors therefor suggest to use a combination of EFA methods for dimensionality assessment and kmeans for item assignment.
From the Cover : Epizootics of wild fish induced by farm fish

www.pnas. org/cgi/content/full/103/42/15506#otherarticles This article has been cited by other articles: E-mail Alerts . click here at the top right corner of the article or Receive free email alerts when new articles cite this article sign up in the box Subspecialty Collections www.pnas. org/cgi/collection/sustainability_sci Sustainability Science collection(s): This article, along with others on similar topics, appears in the following
Effects of All-frans-Retinoic Acid on the Dorsal Skin of: Hairless Dogs

Daily topical treatment with all-trans-retinoic acid (t-RA; 0.1% t-RA solution or 0.05% t-RA cream) was compared with its vehicle with regard to improvement of intrinsically aged skin of hairless descendants of Mexican hairless dogs. After 1 mo of treatment with 0.1% t-RA solution, improvements were noted in skin texture, wrinkling, and pigmentation. Treatment with 0.05% t-RA cream caused an intense adverse effect, retinoid dermatitis. Histologically, 0.1% t-RA solution induced restoration of the skin structure of hairless dogs, resulting in an apparent increase in compaction of the stratum comeum and the epidermal thickness. The epidermis became hyperplastic with definite development of the stratum granulosum. The border between the epidermis and dermis became wavy, and dermal papillae were reconstituted. The 0.1% t-RA solution caused a remarkable decrease in melanin granules. In the dermis, the number of small vessels increased and vasodilation was seen. In sites treated with 0.05% t-RA cream, the stratum corneum became involved in dyskeratotic changes. There was a significantly greater increase in epidermal and granular layer thickness. Necrotic and edematous changes were found in the epidermis, and severe inflammatory reactions were also observed in the dermis. In the t-RA– untreated sites, the structure of the aged skin remained histologically unimproved during the study. The results suggest that hairless dogs are useful laboratory animals for evaluating the effectiveness and side effects of t-RA agents.
Location- and Query-Aware Modeling of Browsing and Click Behavior in Sponsored Search

An online advertisement’s clickthrough rate provides a fundamental measure of its quality, which is widely used in ad selection strategies. Unfortunately, ads placed in contexts where they are rarely viewed—or where users are unlikely to be interested in commercial results—may receive few clicks regardless of their quality. In this article, we model the variability of a user’s browsing behavior for the purpose of click analysis and prediction in sponsored search. Our model incorporates several important contextual factors that influence ad clickthrough rates, including the user’s query and ad placement on search engine result pages. We formally model these factors with respect to the list of ads displayed on a result page, the probability that the user will initiate browsing of this list, and the persistence of the user in browsing the list. We incorporate these factors into existing click models by augmenting them with appropriate query and location biases. Using expectation maximization, we learn the parameters of these augmented models from click signals recorded in the logs of a commercial search engine. To evaluate the performance of the models and to compare them with state-of-the-art performance, we apply standard evaluation metrics, including log-likelihood and perplexity. Our evaluation results indicate that, through the incorporation of query and location biases, significant improvements can be achieved in predicting browsing and click behavior in sponsored search. In addition, we explore the extent to which these biases actually reflect varying behavioral patterns. Our observations confirm that correlations exist between the biases and user search behavior.
A Novel Probabilistic Model for 3D Object Recognition: Spin-Glass Markov Random Fields

This contribution presents a new class of MRF, that is inspired by methods of statistical physics. The new energy function assumes full-connectivity in the neighborhood system and thus solves the modeling problems of MRF in the case of irregular sites. Moreover, it is defined independently from the considered application; this makes it possible to avoid the use of a search algorithm for the energy minima, since those and their analytical properties are provided by theory. Experiments were performed on a database of 12 Objects using multidimensional receptive field histograms. We achieved a recognition rate of 98.33%.
Protein levels of heme oxygenase‐1 during reperfusion in human kidney transplants with delayed graft function

Abstract: Introduction: Delayed graft function (DGF) as a consequence of ischemia reperfusion injury (IRI) is associated with a decrease in long‐term allograft survival. Heme oxygenase‐1 (HO‐1) is a stress responsive gene that is highly expressed in multiple pathological processes. The aim of our study was to analyze whether HO‐1 protein levels in human kidney transplants during IRI correlate with the incidence of DGF.
PKCα and HMGB1 antagonistically control hydrogen peroxide-induced poly-ADP-ribose formation

Harmful oxidation of proteins, lipids and nucleic acids is observed when reactive oxygen species (ROS) are produced excessively and/or the antioxidant capacity is reduced, causing ‘oxidative stress’. Nuclear poly-ADP-ribose (PAR) formation is thought to be induced in response to oxidative DNA damage and to promote cell death under sustained oxidative stress conditions. However, what exactly triggers PAR induction in response to oxidative stress is incompletely understood. Using reverse phase protein array (RPPA) and in-depth analysis of key stress signaling components, we observed that PAR formation induced by H2O2 was mediated by the PLC/IP3R/Ca2+/PKCα signaling axis. Mechanistically, H2O2-induced PAR formation correlated with Ca2+-dependent DNA damage, which, however, was PKCα-independent. In contrast, PAR formation was completely lost upon knockdown of PKCα, suggesting that DNA damage alone was not sufficient for inducing PAR formation, but required a PKCα-dependent process. Intriguingly, the loss of PAR formation observed upon PKCα depletion was overcome when the chromatin structure-modifying protein HMGB1 was co-depleted with PKCα, suggesting that activation and nuclear translocation of PKCα releases the inhibitory effect of HMGB1 on PAR formation. Together, these results identify PKCα and HMGB1 as important co-regulators involved in H2O2-induced PAR formation, a finding that may have important relevance for oxidative stress-associated pathophysiological conditions.
In Vivo Effect of Recombinant Human Granulocyte Colony-Stimulating Factor on Neutrophilic Expression of CD11b in Septic Neonates: A Randomized Controlled Trial

Neonates are susceptible to septicemia secondary to quantitative and qualitative neutrophilic defects. Granulocyte colony-stimulating factor (G-CSF) stimulates myeloid progenitor cell proliferation and induces selective neutrophil functions. The authors aimed to evaluate the effect of G-CSF administration in septic neonates on neutrophil production and CD11b expression. Sixty septic neonates were randomized to receive intravenous G-CSF 10 μg/kg/day for 3 days (G-CSF group, n = 30), or not to receive G-CSF (non–G-CSF group, n = 30). Thirty healthy newborns were included as controls. Laboratory investigations included complete blood count, C-reactive protein, blood culture, renal and liver function tests, and assessment of neutrophilic expression of CD11b. Total leukocytes count (TLC), absolute neutrophil count (ANC), and immature myeloid cell count in G-CSF group showed significant difference between post–and pre–G-CSF levels. TLC, ANC, immature myeloid cell count and immature/total myeloid cells ratio were higher in G-CSF group compared to non–G-CSF group on days 1 and 3. Higher neutrophilic expression of CD11b was reported in both septic groups on day 0 compared to control group. On day 5, CD11b was higher in G-CSF group than non–G-CSF group. G-CSF improved CD11b% in neutropenic and non-neutropenic septic neonates. No significant difference was found between pre- and posttreatment renal and liver function tests. Lower duration of antibiotic intake and hospitalization was observed in G-CSF group compared to non–G-CSF group. G-CSF administration as an adjuvant therapy for neonatal septicemia, whether neutropenic or not, improves neutrophilic count and function and contributed to early healing from sepsis.
Localization of SPARC in developing, mature, and chronically injured human allograft kidneys.

BACKGROUND The matricellular protein SPARC (secreted protein acidic and rich in cysteine) is expressed during development, tissue remodeling and repair. It functions as an endogenous inhibitor of cell proliferation, regulates angiogenesis, regulates cell adhesion to extracellular matrix, binds cytokines such as platelet derived growth factor and stimulates transforming growth factor-beta (TGF-beta) production. This study describes the expression of SPARC during human renal development, in normal kidneys and during renal allograft rejection. METHODS A total of 60 renal specimens, including normal areas from tumor nephrectomies (N = 24), fetal kidneys (N = 27) and explanted renal allografts (N = 9), were included in the study. SPARC protein was localized by immunohistochemistry using two different antibodies. On consecutive sections SPARC mRNA was detected by in situ hybridization. RESULTS In the normal adult kidney SPARC protein was expressed by visceral and parietal epithelial cells, collecting duct epithelium (CD), urothelium, smooth muscle cells of muscular arteries and focally in interstitial cells. During renal development immature glomeruli demonstrated a polarized SPARC expression in visceral epithelial cells at their surface abutting the capillary basement membranes. In the fully differentiated glomeruli the expression pattern mirrored that of the adult kidney. Furthermore, SPARC was abundantly expressed by derivatives of the ureteric bud, and smooth muscle cells of arterial walls. During chronic allograft rejection SPARC is expressed in neointimal arterial smooth muscle cells, infiltrating inflammatory cells as well as by interstitial myofibroblasts in areas of interstitial fibrosis. SPARC mRNA synthesis detected by in situ hybridization mirrored these protein expression patterns. CONCLUSION These studies co-localize SPARC to several sites of renal injury previously shown to be sites of PDGF B-chain expression and/or activity. We speculate that SPARC could function as an accessory molecule in chronic PDGF-mediated sclerosing interstitial and vascular injury. SPARC localization to glomerular epithelial cells corresponds to similar findings in rodents, and may reflect its role in cell adhesion and /or regulation of cell shape.
Routing of internalized ricin and ricin conjugates to the Golgi complex

Receptor-mediated endocytosis and intracellular routing of native ricin, and of ricin conjugated to colloidal gold (Ri-Au) and to horseradish peroxidase (Ri-HRP), have been studied in cultured MCF-7 and Vero cells by electron microscopical techniques including serial section analysis. Both native ricin, as demonstrated by immunoperoxidase cytochemistry, and the ricin conjugates were internalized via a common coated pit-coated vesicle pathway to reach vacuolar and tubulo-vesicular portions of the endosomal system. In addition, native ricin and a purified monovalent fraction of Ri-HRP reached distinct Golgi cisterns, whereas Ri-Au and polyvalent Ri-HRP did not. The results delineate intracellular routing of native ricin and compare it with the routing of different ricin conjugates. Moreover, our study shows that conjugates of a particular ligand (ricin) and various probes (e.g., gold and peroxidase), may be handled differently by cells. Sorting apparently takes place in the endosomal system, allowing some but not other molecules to reach Golgi elements. This sorting seems to depend on the valency of the ricin conjugate.
QT interval of the ECG, heart rate and arterial pressure during anaesthetic induction: comparative effects of alfentanil and esmolol

In a double‐blind study the effect of esmolol and alfentanil on the QT interval of the ECG corrected by the heart rate (QTc), heart rate and arterial pressure during anaesthetic induction was studied in 59 oxycodone‐ and atropine‐premedicated ASA class I‐(II) patients with a mean age of 26 yr (range 15–50 yr). The patients were randomly allocated to one of the four groups: saline, esmolol 2 mg · kg‐1, esmolol 3 mg · kg‐1 or alfentanil 0.03 mg·kg‐1. Both doses of esmolol prevented the prolongation of the QTc interval after thiopental and suxamethonium, but not after laryngoscopy and intubation. Alfentanil prevented the prolongation of the QTc interval following thiopental, suxamethonium and laryngoscopy but not after intubation. Esmolol did not prevent the increase in the heart rate and arterial pressure in response to laryngoscopy and intubation. No cardiovascular responses to laryngoscopy and intubation occurred in the patients treated with alfentanil. No cardiac arrhythmias occurred in the esmolol 3 mg·kg‐1 group, whereas the frequency of ventricular ectopic beats was 40% in the saline group and 13–20% m the other groups.
Differential Growth and Development of the Upper and Lower Human Thorax

The difficulties in quantifying the 3D form and spatial relationships of the skeletal components of the ribcage present a barrier to studies of the growth of the thoracic skeleton. Thus, most studies to date have relied on traditional measurements such as distances and indices from single or few ribs. It is currently known that adult-like thoracic shape is achieved early, by the end of the second postnatal year, with the circular cross-section of the newborn thorax transforming into the ovoid shape of adults; and that the ribs become inclined such that their anterior borders come to lie inferior to their posterior. Here we present a study that revisits growth changes using geometric morphometrics applied to extensive landmark data taken from the ribcage. We digitized 402 (semi) landmarks on 3D reconstructions to assess growth changes in 27 computed tomography-scanned modern humans representing newborns to adults of both sexes. Our analyses show a curved ontogenetic trajectory, resulting from different ontogenetic growth allometries of upper and lower thoracic units. Adult thoracic morphology is achieved later than predicted, by diverse modifications in different anatomical regions during different ontogenetic stages. Besides a marked increase in antero-posterior dimensions, there is an increase in medio-lateral dimensions of the upper thorax, relative to the lower thorax. This transforms the pyramidal infant thorax into the barrel-shaped one of adults. Rib descent is produced by complex changes in 3D curvature. Developmental differences between upper and lower thoracic regions relate to differential timings and rates of maturation of the respiratory and digestive systems, the spine and the locomotor system. Our findings are relevant to understanding how changes in the relative rates of growth of these systems and structures impacted on the development and evolution of modern human body shape.
Sympathetic innervation and α‐adrenoceptor profile of blood vessels in the posterior region of the rabbit knee joint

1 Experiments were performed to determine the nature of adrenoceptors mediating neurally‐induced vasoconstriction of blood vessels in the posterior region of the rabbit knee joint capsule. 2 Electrical stimulation of the posterior articular nerve resulted in frequency‐dependent vasoconstriction which was maximal at 10 Hz. This response was mediated predominantly by α2‐adrenoceptors as it was only slightly reduced by prazosin administration and was not only abolished but converted into a dilator response by the α2‐adrenoceptor antagonist rauwolscine. Further experiments with another specific α1‐adrenoceptor antagonist YM‐12617 showed that the frequency‐response curve in the presence of this antagonist did not differ significantly from control. 3 Neurally‐induced vasoconstriction did not appear to have a purinergic component as it was unaffected by the P2x‐purinoceptor desensitiser α,β methylene ATP. 4 The rank‐order of potency of α‐adrenoceptor agonists given as a bolus by close intra‐arterial injection was: adrenaline = UK‐14304 > clonidine > phenylephrine, suggesting that the vasoconstrictor effects were mediated predominantly by postjunctional α2‐adrenoceptors. 5 The α2‐adrenoceptor antagonist rauwolscine converted the constrictor response to close intra‐arterial injection of adrenaline into a dilator response. The vasoconstrictor responses to UK‐14304, clonidine and phenylephrine were substantially inhibited by rauwolscine. The α1‐adrenoceptor antagonist prazosin failed to inhibit the vasoconstrictor responses to adrenaline, clonidine and UK‐14304 and resulted in enhancement of their constrictor effects. 6 The enhancement of the responses to the α1 and α2 agonists by prazosin appeared to be specifically related to this agent as administration of YM‐12617 did not show such enhancement. The dose‐response curves to both clonidine and UK‐14304 in the presence of YM‐12617 did not differ significantly from control responses. Responses to phenylephrine were significantly reduced by YM‐12617, indicating the presence of post‐junctional α1‐adrenoceptors. 7 These results show almost complete reversal of the adrenoceptor profile compared to results obtained in an earlier in vitro study, where responses were mediated predominantly by α1‐adrenoceptors with a small population of postjunctional α2‐adrenoceptors (Ferrell & Khoshbaten, 1989). This suggests that the differing environment in vitro may not completely reflect the conditions prevailing in vivo.
Utility of B-natriuretic peptide as a rapid, point-of-care test for screening patients undergoing echocardiography to determine left ventricular dysfunction.

BACKGROUND Although echocardiography is an important tool for making the diagnosis of left ventricular (LV) dysfunction, the cost of this procedure limits its use as a routine screening tool for this purpose. Brain natriuretic peptide (BNP) accurately reflects ventricular pressure, and preliminary studies have found it to be highly sensitive and highly specific in diagnosing congestive heart failure in the emergency department. We hypothesized that BNP might therefore be useful as a screening tool before echocardiography in patients with suspected LV dysfunction. METHODS Subjects included patients referred for echocardiography to evaluate the presence or absence of LV dysfunction. Patients with known LV dysfunction were excluded from analysis. BNP was measured by a point-of-care immunoassay (Biosite Diagnostics, San Diego, Calif). The results of BNP levels were blinded from cardiologists making the assessment of LV function. Patients were divided into those with normal ventricular function, abnormal systolic ventricular function, abnormal diastolic function, and evidence of both systolic and diastolic dysfunction. RESULTS Two hundred patients in whom LV function was unknown were studied. In the 105 patients (53%) whose ventricular function was subsequently determined to be normal by echocardiography, BNP levels averaged 37 +/- 6 pg/mL. This was significantly less than in those patients with either ultimate diastolic dysfunction (BNP 391 +/- 89 pg/mL (P <.001) or systolic dysfunction (BNP 572 +/- 115 pg/mL (P <.001). A receiver-operator characteristic curve showing the sensitivity and specificity of BNP against the echocardiography diagnosis revealed the area under the curve (accuracy) was 0.95. At a BNP level of 75 pg/mL was 98% specific for detecting the presence or absence of LV dysfunction by echocardiography. CONCLUSIONS A simple, rapid test for BNP, which can be performed at the bedside or in the clinic, can reliably predict the presence or absence of LV dysfunction on echocardiogram. The data indicate that BNP may be an excellent screening tool for LV dysfunction and may, in fact, preclude the need for echocardiography in many patients.
Predictors of Discordant Reports of Sexual and HIV/Sexually Transmitted Infection Risk Behaviors Among Heterosexual Couples

Objectives: Assessments undertaken as part of couple-based HIV/sexually transmitted infection (STI) prevention intervention studies offer opportunities to expand our understanding of couple reporting of sexual and HIV/STI risk behavior. Increases in heterosexual transmission of HIV worldwide support more attention on the quality and use of couple-level sexual risk assessment. Study Design: This study examined interpartner concordance of self-reported sexual behaviors and HIV/STI risk behaviors among 217 women and their main male sexual partners at high risk for HIV/STI transmission and further explored specific individual and relationship characteristics by partner gender associated with discordant reporting of sexual and HIV/STI risk behaviors. Results: Consistent with prior studies, findings suggest fair to substantial agreement between partners on reports of most sexual and HIV/STI risk behavior, but only poor to fair agreement on reports of concurrent sexual behaviors and drug or alcohol use. Factors significantly associated with discordant reporting of sexual behaviors included length of couple relationship, level of relationship satisfaction, female partner’s marital status, and male partner’s HIV status, ethnicity, and age. Conclusions: Individual- and relationship-level factors predicting discordant partner reports of sexual and sexual risk behaviors highlight an opportunity to improve couple assessment by anticipating such discrepancies and developing effective mechanisms of quality assurance to avoid, address, or better explain such discordance in couple data sets.