Miracle-dz/UniFAR-FTUs huggingface dataset:
Soluble urokinase plasminogen activator receptor as a useful biomarker to predict the response to adalimumab in patients with rheumatoid arthritis in a Japanese population.

OBJECTIVES To determine whether soluble urokinase plasminogen activator receptor is a useful biomarker to predict the response to adalimumab (ADA) in Japanese patients with rheumatoid arthritis. METHODS Rheumatoid arthritis (RA) patients administrated ADA (n=51) were classified as good responders (n=18) or nonresponders (n=9) according to the EULAR response criteria after 8 weeks of bi-weekly ADA administration. We examined the expression of cytokines and chemokines in these groups by antibody array methods. Positive results obtained by antibody array methods were further confirmed by ELISA. RESULTS Antibody array has identified that the macrophage migration inhibitory factor (MIF), vascular endothelial growth factor (VEGF) and soluble urokinase plasminogen activator receptor (uPAR) decreased in the good responders to ADA whereas these changes were not observed in the non-responders. The decrement of serum uPAR was confirmed by ELISA in the good responders to ADA. Furthermore, serum uPAR at baseline was significantly high in non-responders compared with good responders. CONCLUSIONS An antibody array is convenient for screening the expression of proteins of interest. Examination of serum uPAR at baseline and thereafter may be useful as a predictive biomarker for primary failure toward ADA in patients with RA.
The efficacy and safety of probiotics in people with cancer: a systematic review.

BACKGROUND Probiotics are living microorganisms that are generally thought of as being beneficial to the recipient. They have been shown to be effective in people with acute infectious diarrhoea, and cost-effective in antibiotic-associated diarrhoea. Probiotics may have a role in people with cancer, as various cancer treatments often lead to diarrhoea. However, as people with cancer are often immunocompromised, it is important to assess for adverse events (AEs) such as infection, which could potentially be a consequence of deliberate ingestion of living microorganisms. DESIGN A systematic review was carried out to collect, analyse and synthesise all available data on the efficacy and safety of probiotics in people with cancer (PROSPERO registration: CRD42012003454). Randomised, controlled trials, identified through screening multiple databases and grey literature, were included for analysing efficacy, while all studies were included for the analysis of safety of probiotics. Primary outcomes were the reduction in duration, severity and incidence of antibiotic-associated diarrhoea and chemotherapy-associated diarrhoea, and AEs, especially probiotic-associated infection. Where possible, data were combined for meta-analysis by a random-effects model, assessing causes of heterogeneity, including differences in strains, dosage and patient characteristics. RESULTS Eleven studies (N = 1557 participants) were included for assessing efficacy. Results show that probiotics may reduce the severity and frequency of diarrhoea in patients with cancer and may reduce the requirement for anti-diarrhoeal medication, but more studies are needed to assess the true effect. For example comparing probiotic use to control 25 groups on effect on Common Toxicity Criteria ≥2 grade diarrhoea, odds ratio (OR) = 0.32 [95% confidence interval (CI) of 0.13-0.79; P = 0.01]. Seventeen studies (N = 1530) were included in the safety analysis. Five case reports showed probiotic-related bacteraemia/fungaemia/positive blood cultures. CONCLUSIONS Probiotics may be a rare cause of sepsis. Further evidence needs to be collated to determine whether probiotics provide a significant overall benefit for people with cancer.
Angiotensinogen levels in the brain and cerebrospinal fluid of the genetically hypertensive rat.

The present experiments were designed to document changes in the regional distribution of angiotensinogen in the rat brain with the development of hypertension in spontaneously hypertensive rats (SHR) relative to age-matched normotensive Wistar-Kyoto rats (WKY). Levels of angiotensinogen were measured in discrete brain nuclei and cerebrospinal fluid from rats at 4, 7, and 16 weeks of age and in cerebrospinal fluid obtained by cisternal puncture at 7 and 16 weeks. Age-dependent changes in angiotensinogen were found, with levels higher in both strains at 4 weeks of age compared with 7 or 16 weeks. In contrast, plasma levels of angiotensinogen were essentially the inverse of the brain levels, low at 4 weeks and higher at 7 and 16 weeks. Levels in a number of regions adjacent to the rostral third ventricle from the 4-week-old SHR (prehypertensive phase) were significantly elevated relative to the WKY (p less than 0.05), while levels in the amygdala and posterior hypothalamus were significantly lower in the SHR (p less than 0.05). In 7-week-old rats (evolving phase), levels in nine brain regions were significantly elevated in the SHR relative to the WKY and included the nucleus tractus solitarii (p less than 0.01). Unlike the prehypertensive and evolving phases, in 16-week-old rats (maintenance phase) only two brain areas, the nucleus of the diagonal band and the lateral hypothalamus, had significantly elevated levels in the SHR (p less than 0.05). Cerebrospinal fluid levels of angiotensinogen did not correlate well with brain levels of angiotensinogen. (ABSTRACT TRUNCATED AT 250 WORDS)
System identification of buildings by wave travel time analysis and layered shear beam models—Spatial resolution and accuracy

A previously explored method for one‐dimensional structural system identification and earthquake damage detection in buildings, based on measuring wave travel time through the structure and its changes, is formalized, and its spatial resolution and accuracy are analyzed. The method identifies the velocity of propagation of shear waves in the structure as function of height. The wave travel time is measured from impulse responses obtained from recorded response at different locations in the structure. The main advantages of this SHM method over other methods are its robustness in application to real buildings and large amplitude response, insensitivity to the effects of soil–structure interaction, and local in nature achieved with relatively small number of sensors. The identification is based on a layered shear beam model of the building. In this paper, analytical impulse response functions are presented for such model, which provide theoretical basis to define identification algorithms. The derivation of one such algorithm, which involves approximations, from the exact wave propagation solution of the model is presented, and its spatial resolution and accuracy are critically examined. Termed here ‘direct algorithm’, it involves measuring the pulse time shifts and amplitudes and identifies shear wave velocities and quality factor Q in the layers. Various issues identified, e.g. the trade‐off between accuracy and detail of the identification, are illustrated on a full‐scale densely instrumented nine‐story RC building (Millikan Library in Pasadena, CA, USA, excited by 2002 Yorba Linda earthquake). Copyright © 2012 John Wiley & Sons, Ltd.
Physiologic isolation of the canine proximal fibular epiphysis on a vascular pedicle

In order to create a model for epiphyseal growth plate transplantation by microvascular technique, a well‐defined donor site was established. Dissection of latex‐injected adult and juvenile dogs established the vascular supply to the proximal canine fibula. By isolating 7 cm of proximal fibula on the popliteal vessels, the nutrient supply to the epiphyses, metaphysis, and diaphysis is retained. This preserves the nutrient arterial supply to the fibula originating from the cranial tibial artery, the caudal tibial artery, and the small blood vessels from these to the epiphysis. Perfusion of the graft through the defined vascular pedicle was confirmed using 141Ce‐labeled microspheres. These results showed a perfusion of the established graft that was as great as or greater than the control, unoperated side. It is concluded that the technique described for isolation can be used for developing a model for vascularized transplantation of epiphyseal growth cartilage in canines.
Zinc Modulation of Water Permeability Reveals that Aquaporin 0 Functions as a Cooperative Tetramer

We previously showed that the water permeability of AQP0, the water channel of the lens, increases with acid pH and that His40 is required (Németh-Cahalan, K.L., and J.E. Hall. 2000. J. Biol. Chem. 275:6777–6782; Németh-Cahalan, K.L., K. Kalman, and J.E. Hall. 2004. J. Gen. Physiol. 123:573–580). We have now investigated the effect of zinc (and other transition metals) on the water permeability of AQP0 expressed in Xenopus oocytes and determined the amino acid residues that facilitate zinc modulation. Zinc (1 mM) increased AQP0 water permeability by a factor of two and prevented any additional increase induced by acid pH. Zinc had no effect on water permeability of AQP1, AQP4 or MIPfun (AQP0 from killifish), or on mutants of AQP1 and MIPfun with added external histidines. Nickel, but not copper, had the same effect on AQP0 water permeability as zinc. A fit of the concentration dependence of the zinc effect to the Hill equation gives a coefficient greater than three, suggesting that binding of more than one zinc ion is necessary to enhance water permeability. His40 and His122 are necessary for zinc modulation of AQP0 water permeability, implying structural constraints for zinc binding and functional modulation. The change in water permeability was highly sensitive to a coinjected zinc-insensitive mutant and a single insensitive monomer completely abolished zinc modulation. Our results suggest a model in which positive cooperativity among subunits of the AQP0 tetramer is required for zinc modulation, implying that the tetramer is the functional unit. The results also offer the possibility of a pharmacological approach to manipulate the water permeability and transparency of the lens.
Citadel: Efficiently Protecting Stacked Memory from Large Granularity Failures

Stacked memory modules are likely to be tightly integrated with the processor. It is vital that these memory modules operate reliably, as memory failure can require the replacement of the entire socket. To make matters worse, stacked memory designs are susceptible to newer failure modes (for example, due to faulty through-silicon vias, or TSVs) that can cause large portions of memory, such as a bank, to become faulty. To avoid data loss from large-granularity failures, the memory system may use symbol-based codes that stripe the data for a cache line across several banks (or channels). Unfortunately, such data-striping reduces memory level parallelism causing significant slowdown and higher power consumption. This paper proposes Citadel, a robust memory architecture that allows the memory system to retain each cache line within one bank, thus allowing high performance, lower power and efficiently protects the stacked memory from large-granularity failures. Citadel consists of three components, TSV-Swap, which can tolerate both faulty data-TSVs and faulty address-TSVs, Tri Dimensional Parity (3DP), which can tolerate column failures, row failures, and bank failures, and Dynamic Dual Granularity Sparing (DDS), which can mitigate permanent faults by dynamically sparing faulty memory regions either at a row granularity or at a bank granularity. Our evaluations with real-world data for DRAM failures show that Citadel provides performance and power similar to maintaining the entire cache line in the same bank, and yet provides 700x higher reliability than Chip Kill-like ECC codes.
Screen Printed Carbon Electrode Based Electrochemical Immunosensor for the Detection of Dengue NS1 Antigen

An electrochemical immunosensor modified with the streptavidin/biotin system on screen printed carbon electrodes (SPCEs) for the detection of the dengue NS1 antigen was developed in this study. Monoclonal anti-NS1 capture antibody was immobilized on streptavidin-modified SPCEs to increase the sensitivity of the assay. Subsequently, a direct sandwich enzyme linked immunosorbent assay (ELISA) format was developed and optimized. An anti-NS1 detection antibody conjugated with horseradish peroxidase enzyme (HRP) and 3,3,5,5'-tetramethybezidine dihydrochloride (TMB/H2O2) was used as an enzyme mediator. Electrochemical detection was conducted using the chronoamperometric technique, and electrochemical responses were generated at −200 mV reduction potential. The calibration curve of the immunosensor showed a linear response between 0.5 µg/mL and 2 µg/mL and a detection limit of 0.03 µg/mL. Incorporation of a streptavidin/biotin system resulted in a well-oriented antibody immobilization of the capture antibody and consequently enhanced the sensitivity of the assay. In conclusion, this immunosensor is a promising technology for the rapid and convenient detection of acute dengue infection in real serum samples.
Temporal Bone Histopathology Related to Cochlear Implantation in Congenital Malformation of the Bony Cochlea

Hypothesis Histopathologic findings in temporal bones with congenital malformations of the bony cochlea may provide insight into cochlear implantation planning, surgical approach, and complications. Background Patients with congenitally malformed cochleae account for an increasing percentage of candidates for cochlear implantation. Few studies on the relationship between histopathologic findings of temporal bones with malformation of the bony cochlea and cochlear implantation have been reported. Methods We studied 21 temporal bones from 12 cases with congenital malformations of the bony cochlea. Ages ranged from stillborn to 50 years. Length of the cochleae and dimensions of facial recesses were measured with light microscopy. Other malformations associated with a shortened cochlea were determined, emphasizing how they affect cochlear implantation. Results The average length of the malformed cochlear duct was 22.84 ± 0.69 mm. Average dimensions of facial recesses were not significantly different between malformed cochleae and the controls. Other malformations included enlarged cochlear aqueduct (43%), abnormal facial nerve course (57%), enlarged vestibular aqueduct (52%), aplasia of the middle ear (19%), malformed ossicles (67%), abnormal oval window (57%), and abnormal round window (29%). Conclusion A shortened cochlear duct may cause an incomplete insertion of the implant electrode. Because dimensions of the facial recesses are similar to normal cases, a facial recess surgical approach is recommended. An enlarged cochlear aqueduct may cause perilymphatic oozing or gushing on fenestration of the cochlea. An anomalous course of the facial nerve is a common finding. Tympanic malformations such as round and oval window deformities and small middle ear cleft should be noted preoperatively to better guide surgery.
Partially labeled topic models for interpretable text mining

Abstract Much of the world's electronic text is annotated with human-interpretable labels, such as tags on web pages and subject codes on academic publications. Effective text mining in this setting requires models that can flexibly account for the textual patterns that underlie the observed labels while still discovering unlabeled topics. Neither supervised classification, with its focus on label prediction, nor purely unsupervised learning, which does not model the labels explicitly, is appropriate. In this paper, we present two new partially supervised generative models of labeled text, Partially Labeled Dirichlet Allocation (PLDA) and the Partially Labeled Dirichlet Process (PLDP). These models make use of the unsupervised learning machinery of topic models to discover the hidden topics within each label, as well as unlabeled, corpus-wide latent topics. We explore applications with qualitative case studies of tagged web pages from del.icio. us and PhD dissertation abstracts, demonstrating improved model interpretability over traditional topic models. We use the many tags present in our del.icio. us dataset to quantitatively demonstrate the new models' higher correlation with human relatedness scores over several strong baselines.
Cpa, the Outer Membrane Protease of Cronobacter sakazakii, Activates Plasminogen and Mediates Resistance to Serum Bactericidal Activity

ABSTRACT Cronobacter spp. are emerging neonatal pathogens in humans, associated with outbreaks of meningitis and sepsis. To cause disease, they must survive in blood and invade the central nervous system by penetrating the blood-brain barrier. C. sakazakii BAA-894 possesses an ∼131-kb plasmid (pESA3) that encodes an outer membrane protease (Cpa) that has significant identity to proteins that belong to the Pla subfamily of omptins. Members of this subfamily of proteins degrade a number of serum proteins, including circulating complement, providing protection from the complement-dependent serum killing. Moreover, proteins of the Pla subfamily can cause uncontrolled plasmin activity by converting plasminogen to plasmin and inactivating the plasmin inhibitor α2-antiplasmin (α2-AP). These reactions enhance the spread and invasion of bacteria in the host. In this study, we found that an isogenic cpa mutant showed reduced resistance to serum in comparison to its parent C. sakazakii BAA-894 strain. Overexpression of Cpa in C. sakazakii or Escherichia coli DH5α showed that Cpa proteolytically cleaved complement components C3, C3a, and C4b. Furthermore, a strain of C. sakazakii overexpressing Cpa caused a rapid activation of plasminogen and inactivation of α2-AP. These results strongly suggest that Cpa may be an important virulence factor involved in serum resistance, as well as in the spread and invasion of C. sakazakii.
Caprini Scores, Risk Stratification, and Rivaroxaban in Plastic Surgery: Time to Reconsider Our Strategy

Summary: Limited data are available regarding the pathophysiology of venous thromboembolism in plastic surgery patients. In an effort to identify patients at greater risk, some investigators promote individual risk assessment using Caprini scores. However, these scores do not correlate with relative risk values. Affected patients cannot be reliably predicted (97% false positive rate). Caprini scores make many body contouring patients candidates for chemoprophylaxis, an intervention that introduces risks related to anticoagulation. Caprini has financial conflicts with several companies that manufacture products such as enoxaparin, commonly used for chemoprophylaxis. Rivaroxaban, taken orally, has been used by some plastic surgeons as an alternative to enoxaparin injections. However, this medication is not United States Food and Drug Administration approved for venous thromboembolism prophylaxis in plastic surgery patients, and a reversal agent is unavailable. This article challenges the prevailing wisdom regarding individual risk stratification and chemoprophylaxis. Alternative methods to reduce risk for all patients include safer anesthesia methods and Doppler ultrasound surveillance. Clinical findings alone are unreliable in diagnosing deep venous thromboses. Only by using a reliable diagnostic tool such as Doppler ultrasound are we able to learn more about the natural history of this problem in our patients. Such knowledge is likely to better inform our treatment recommendations.
Effects of hand gestures on auditory learning of second-language vowel length contrasts.

PURPOSE Research has shown that hand gestures affect comprehension and production of speech at semantic, syntactic, and pragmatic levels for both native language and second language (L2). This study investigated a relatively less explored question: Do hand gestures influence auditory learning of an L2 at the segmental phonology level? METHOD To examine auditory learning of phonemic vowel length contrasts in Japanese, 88 native English-speaking participants took an auditory test before and after one of the following 4 types of training in which they (a) observed an instructor in a video speaking Japanese words while she made syllabic-rhythm hand gesture, (b) produced this gesture with the instructor, (c) observed the instructor speaking those words and her moraic-rhythm hand gesture, or (d) produced the moraic-rhythm gesture with the instructor. RESULTS All of the training types yielded similar auditory improvement in identifying vowel length contrast. However, observing the syllabic-rhythm hand gesture yielded the most balanced improvement between word-initial and word-final vowels and between slow and fast speaking rates. CONCLUSIONS The overall effect of hand gesture on learning of segmental phonology is limited. Implications for theories of hand gesture are discussed in terms of the role it plays at different linguistic levels.
Innervation of the cricothyroid muscle by the recurrent laryngeal nerve

The recurrent laryngeal nerve (RLN) and the external branch of the superior laryngeal nerve (SLN) are generally thought to innervate the endolaryngeal muscles and the cricothyroid muscle (CTM), respectively. Meticulous anatomic studies found communication between these nerves (ie, the human communicating nerve). In this study, we report the innervation of the CTM by the RLN.
Protecting Biometric Templates With Sketch: Theory and Practice

Secure storage of biometric templates has become an increasingly important issue in biometric authentication systems. We study how secure sketch, a recently proposed error-tolerant cryptographic primitive, can be applied to protect the templates. We identify several practical issues that are not addressed in the existing theoretical framework, and show the subtleties in evaluating the security of practical systems. We propose a general framework to design and analyze a secure sketch for biometric templates, and give a concrete construction for face biometrics as an example. We show that theoretical bounds have their limitations in practical schemes, and the exact security of the system often needs more careful investigations. We further discuss how to use secure sketch in the design of multifactor authentication systems that allow easy revocation of user credentials.
Behaviour and welfare of individual laying hens in a non-cage system

1. A leg band containing a transponder was fitted to 80 birds in a perchery containing 1000 birds. 2. The transponder emitted a unique identification number when a bird walked on one of 8 flat antennae on the floor. The recording apparatus was used to measure the amount of time that each of the tagged birds spent on the slatted and littered areas in a 6-week period. 3. Some birds spent long periods of time on the slats, possibly as a means of avoiding repeated attacks. Duration on the slats was greatest in birds with the worst (as opposed to better) feather scores of the head, back and tail regions. 4. Birds that spent long periods on the slats were lighter than other birds at both 39 weeks of age and 72 weeks of age and had greater back, head and tail feather damage, consistent with these birds being victims of pecking. 5. Tagged birds received a social avoidance test outside the perchery at 39 weeks of age, which suggested that birds retreated to the slats in response to pecks rather than just to close proximity to other birds. 6. The failure to find that duration on the slats was related to anatomical indicators of stress (liver, spleen and bursa of Fabricius) suggests that retreating to the slats following pecking attenuates physiological stress responses. 7. We conclude that the provision of areas where birds in a large group can avoid pecking may improve the welfare of a minority of victimised birds.