Miracle-dz/UniFAR-FTUs huggingface dataset:
MicroRNA Sequence Profiles of Human Kidney Allografts With or Without Tubulointerstitial Fibrosis

Background MicroRNA (miRNA) alterations accompanying interstitial fibrosis and tubular atrophy (IFTA) in kidney allografts may point toward pathologic mechanisms. Small-RNA sequencing provides information on total miRNA abundance and specific miRNA expression and allows analysis of differential expression based on read counts. Methods MiRNA expression profiles of 8 human kidney allograft biopsies (4 IFTA and 4 normal biopsies, discovery set) were characterized using barcoded deep-sequencing of a cDNA library prepared from multiplexed RNA. Statistical analysis of the sequence data guided selection of miRNAs for validation and the levels of selected miRNAs were quantified in 18 biopsies (10 IFTA and 8 normal) using real-time quantitative PCR assays (RT-QPCR). Results Total miRNA content was 50% lower in RNA from IFTA compared with normal biopsies. Global miRNA profiles clustered in partial agreement with diagnosis. Several miRNAs, including miR-21, 142-3p, and 5p and the cluster comprising miR-506 on chromosome X had twofold to sevenfold higher expression in IFTA compared with normal biopsies, whereas miRNA miR-30b and 30c were lower in IFTA biopsies (miR-30a, -30d, -30e, and all respective star sequences showed similar trends). IFTA and normal biopsy distinction was also noted in the pattern of miRNA nucleotide sequence variations. Differentially expressed miRNAs were confirmed on the larger set of allograft biopsies using RT-QPCR, and the levels of miRNAs were found to be associated with allograft function and survival. Conclusion Differentially expressed miRNAs and their predicted targets identified by deep sequencing are candidates for further investigation to decipher the mechanism and management of kidney allograft fibrosis.
Preclinical evaluation of the tyrosine kinase inhibitor SU11248 as a single agent and in combination with "standard of care" therapeutic agents for the treatment of breast cancer.

SU11248 is an oral multitargeted tyrosine kinase inhibitor with antitumor and antiangiogenic activities through targeting platelet-derived growth factor receptor, vascular endothelial growth factor receptor, KIT, and FLT3, the first three of which are expressed in human breast cancer and/or its supporting tissues. The purpose of the present studies was to demonstrate the potent anticancer activity of SU11248 alone or in combination with conventional cytotoxic agents against several distinct preclinical models of breast cancer. SU11248 was administered as a monotherapy to (1) mouse mammary tumor virus-v-Ha-ras mice and 7,12-dimethylbenz(a)anthracene-treated rats bearing mammary tumors and (2) mice bearing human breast cancer xenografts of s.c. MX-1 tumors and osseous metastasis of a MDA-MB-435-derived cell line (435/HAL-Luc). SU11248 was also administered in combination with docetaxel both in xenograft models and in combination with 5-fluorouracil and doxorubicin in the MX-1 model. SU11248 treatment potently regressed growth of mammary cancers in mouse mammary tumor virus-v-Ha-ras transgenic mice (82% regression) and 7,12-dimethylbenz(a)anthracene-induced mammary tumors in rats (99% regression at the highest dose; P < 0.05 for both). This agent also inhibited MX-1 tumor growth by 52%, with markedly enhanced anticancer effects when administered in combination with docetaxel, 5-fluorouracil, or doxorubicin compared with either agent alone (P < 0.05). SU11248 treatment in combination with docetaxel effectively prolonged survival of mice, with 435/HAL-Luc cancer xenografts established in bone compared with either agent alone (P < 0.05). These results demonstrate that SU11248 is effective in preclinical breast cancer models and suggest that it may be useful in the treatment of breast cancer in the clinic.
Identification and mutation analysis of DOC-1R, a DOC-1 growth suppressor-related gene.

The tumor suppressor gene MEN1 and several oncogenes including CCND1/cyclin D1/PRAD1 map to chromosome 11q13. However, molecular and cytogenetic analysis suggests the presence of a second tumor suppressor locus at this chromosome region. We have identified a novel gene from chromosome 11q13, which encodes a protein of 126 amino acids sharing an overall 57% identity with the p12(DOC-1) protein encoded by the DOC-1 gene, the human homolog of hamster putative tumor suppressor doc-1 (deleted in oral cancer-1). We therefore designated the novel gene as DOC-1R for DOC-1-related. The cytogenetic location was confirmed by chromosome fluorescent in situ hybridization. Northern blot analysis indicated that it was expressed in all the tissues examined. DOC-1R protein showed heterogeneous subcellular localization. RT-PCR-SSCP analysis failed to detect deleterious mutations of the DOC-1R transcript in four premalignant oral keratinocyte lines and 20 different cancer cell lines from tumor types which frequently harbor LOH at chromosome 11q13.
Intrauterine Risk Factors for Precocious Atherosclerosis

Evidence from noninvasive ultrasound studies of the neonatal aorta and fetal and early childhood postmortem studies indicates that impaired fetal growth, in utero exposure to maternal hypercholesterolemia, and diabetic macrosomia may all be important risk factors for vascular changes consistent with the earliest physical signs of atherosclerosis. Although the exact mechanisms that underlie these associations remain unclear, animal models have suggested that the use of antioxidant, lipid-lowering, and other innovative therapies may counteract the impact of these intrauterine risk factors for cardiovascular disease. This review summarizes the current evidence for intrauterine factors that have a direct impact on atherosclerosis and provides potential treatment and prevention strategies.
Comparison of Multiple System Combination Techniques for Keyword Spotting

System combination is a common approach to improving results for both speech transcription and keyword spotting—especially in the context of low-resourced languages where building multiple complementary models requires less computational effort. Using state-of-the-art CNN and DNN acoustic models, we analyze the performance, cost, and trade-offs of four system combination approaches: feature combination, joint decoding, hitlist combination, and a novel lattice combination method. Previous work has focused solely on accuracy comparisons. We show that joint decoding, lattice combination, and hitlist combination perform comparably, significantly better than feature combination. However, for practical systems, earlier combination reduces computational cost and storage requirements. Results are reported on four languages from the IARPA Babel dataset.
Hepatitis A vaccination during an outbreak among gay men in Montréal, Canada, 1995–1997

STUDY OBJECTIVE To evaluate an intervention designed to curtail an outbreak of hepatitis A among gay men, especially the young and sexually active, by promoting their free vaccination. DESIGN The study analysed routine passive surveillance data, carried out questionnaire and serological surveys of vaccinees, and surveys among the target population in non-clinical venues. SETTING AND INTERVENTION 15 000 free doses of hepatitis A vaccine were made available through clinics with large gay clienteles, or at gay events, and advertised by various means, in Montréal, Canada, from August 1996 to November 1997. Simultaneous vaccination against hepatitis B (always free for gay men) was also encouraged. PARTICIPANTS Information was obtained from persons with the disease during the epidemic period, a sample of men requesting vaccination, and five community samples of gay men. MAIN RESULTS The outbreak involved 376 gay men and the vaccine was distributed to approximately 10 000. Vaccinees were older than cases, but had many sex partners and comprised more food handlers. Special vaccination clinics at gay events were well attended but did not reach more high risk men than regular medical venues. A self reported vaccine coverage of 49% was achieved, but 26% of vaccinees already had anti-HAV antibodies. Disease incidence declined rapidly during the campaign. CONCLUSIONS The intervention nearly tripled self reported hepatitis A vaccine coverage but its late start precludes proving that it caused the subsequent drop in incidence. However, it also increased hepatitis B vaccination and it is believed it improved links between gay men, public health, clinicians and community groups.
Generalized approximate message passing estimation from quantized samples

Estimation of a vector from quantized linear measurements is a common problem for which simple linear techniques are sometimes greatly suboptimal. This paper summarizes the development of generalized approximate message passing (GAMP) algorithms for minimum mean-squared error estimation of a random vector from quantized linear measurements, notably allowing the linear expansion to be overcomplete or undercomplete and the scalar quantization to be regular or non-regular. GAMP is a recently-developed class of algorithms that uses Gaussian approximations in belief propagation and allows arbitrary separable input and output channels. Scalar quantization of measurements is incorporated into the output channel formalism, leading to the first tractable and effective method for high-dimensional estimation problems involving non-regular scalar quantization. Non-regular quantization is empirically demonstrated to greatly improve rate-distortion performance in some problems with oversampling or with undersampling combined with a sparsity-inducing prior. Under the assumption of a Gaussian measurement matrix with i.i. d. entries, the asymptotic error performance of GAMP can be accurately predicted and tracked through the state evolution formalism.
Towards a Decision Making Support System for the Capacitated Vehicle Routing Problem

Distribution of goods is of importance in logistics and supply chain management. The target of a distribution network is to specify the beneficial way for delivering goods and commodities from supply to demand points. In distribution domain, this activity can usually be viewed as a capacitated vehicle routing problem CVRP. As the CVRP solutions remain computationally intractable, we develop in this paper an interactive routing decision making support system R-DMSS that integrates a swarm based approach into a geographical information system GIS. The empirical experiments include benchmarking instances as well as a case study over the Ezzahra area in Tunisia. The R-DMSS interfaces are presented to better understand the operational aspect of the system.
Total Face, Eyelids, Ears, Scalp, and Skeletal Subunit Transplant Cadaver Simulation: The Culmination of Aesthetic, Craniofacial, and Microsurgery Principles

Background: The application of aesthetic, craniofacial, and microsurgical principles in the execution of face transplantation may improve outcomes. Optimal soft-tissue face transplantation can be achieved by incorporating subunit facial skeletal replacement and subsequent tissue resuspension. The purpose of this study was to establish a reconstructive solution for a full face and scalp burn and to evaluate outcome precision and consistency. Methods: Seven mock face transplants (14 cadavers) were completed in the span of 1 year. Components of the vascularized composite allograft included the eyelids, nose, lips, facial muscles, oral mucosa, total scalp, and ears; and skeletal subunits of the zygoma, nasal bone, and genial segment. Virtual surgical planning was used for osteotomy selection, and to evaluate postoperative precision of hard- and soft-tissue elements. Results: Each transplant experience decreased each subsequent transplant surgical time. Prefabricated cutting guides facilitated a faster dissection of both donor and recipient tissue, requiring minimal alteration to the allograft for proper fixation of bony segments during inset. Regardless of donor-to-recipient size discrepancy, ample soft tissue was available to achieve tension-free allograft inset. Differences between virtual transplant simulation and posttransplant measurements were minimal or insignificant, supporting replicable and precise outcomes. Conclusions: This facial transplant model was designed to optimize reconstruction of extensive soft-tissue defects of the craniofacial region representative of electrical, thermal, and chemical burns, by incorporating skeletal subunits within the allograft. The implementation of aesthetic, craniofacial, and microsurgical principles and computer-assisted technology improves surgical precision, decreases operative time, and may optimize function.
Disruption of an inner arm dynein heavy chain gene results in asthenozoospermia and reduced ciliary beat frequency.

Impaired ciliary and flagellar functions resulting in male infertility and recurrent respiratory tract infections are found in patients suffering from primary ciliary dyskinesia (PCD). In most cases, axonemal defects are present, i.e. PCD patients often lack inner and/or outer dynein arms in their sperm tails and cilia, supporting the hypothesis that mutations in dynein genes may cause PCD. However, to date it is unclear whether mutations in dynein heavy chain genes are responsible for impaired flagellar and ciliary motility in mammals. To elucidate the role of the mouse dynein heavy chain 7 (MDHC7) gene, which encodes a component of the inner dynein arm, we have generated mice lacking this dynein heavy chain isoform. Both MDHC7(+/-) and MDHC7(-/-) mice are viable and show no malformations; however, homozygous males produce no offspring. In comparison to MDHC7(+/-) and wild-type mice the spermatozoa of MDHC7(-/-) mice revealed a dramatic reduced straight line velocity and progressive movement, resulting in the inability of MDHC7-deficient sperm to move from the uterus into the oviduct. Additionally, we measured the beat frequency of tracheal cilia and observed a decrease in the beat frequency of approximately 50% in MDHC7(-/-) mice. The reduction in both ciliary and flagellar motility is not correlated with any gross defects in the axonemal structure. The phenotype of MDHC7(-/-) mice is similar to that observed in some patients suffering from PCD, and our data strongly suggest that in some patients this disease could be due to mutations in the homologous human gene DNAH1 (HDHC7).
Entangling capacity of global phases and implications for the Deutsch-Jozsa algorithm

We investigate the creation of entanglement by the application of phases whose value depends on the state of a collection of qubits. First we give the necessary and sufficient conditions for a given set of phases to result in the creation of entanglement in a state comprising of an arbitrary number of qubits. Then we consider the maximum entanglement generation by global phases. We analyze the creation of entanglement between any two qubits in three-qubit pure and mixed states. We use our result to prove that entanglement is necessary for the Deutsch-Jozsa algorithm to have an exponential advantage over its classical counterpart.
Sleep Restriction and Serving Accuracy in Performance Tennis Players, and Eects of Caeine Sleep Restriction, Serving Accuracy in Performance Tennis Players, and Effects of Caffeine L a Reyner & J a Horne

• This is the author's version of a work that was accepted for publication in Physiology and Behavior. In its present form it has the following title: `Sleep restriction, serving accuracy in performance tennis players, and eects of caeine'. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reected in this document. Changes may have been made to this work since it was submitted for publication. A denitive version was subsequently published at: Abstract Athletes often lose sleep on the night before a competition. Whilst it is unlikely that sleep loss will impair sports mostly relying on strength and endurance, little is known about potential effects on sports involving psychomotor performance requiring high level cognitive skills necessitating judgement and accuracy, as in tennis, and where caffeine is 'permitted''. Two studies were undertaken on the effects of 5h sleep (33%) restriction versus normal sleep, on an objective measure of serving accuracy in semi-professional tennis players. Testing (14:00h-16:00h) for both studies comprised 40 serves into a (1.8m x 1.1m) 'service box' diagonally, over the net. Study 2 was identical to that of Study 1, except that there was an extra sleep restriction condition. All conditions involved a sugar free drink given 30 min before testing, but with the drink for one sleep restriction containing 80mg caffeine (double blind). Study 1 comprised 16 men and women, in a within Ss counterbalanced design (normal versus sleep restriction). Study 2 involved 12 different men and women undergoing three conditions in a latin square design. Conditions were as for Study 1, with a replicated sleep restriction. All conditions incorporated a sugar-free drink given 30 min before testing, with one restriction including 80mg caffeine (double blind). Both studies showed significant impairments to serving accuracy following sleep restriction, particularly with women. At this dose, caffeine had no beneficial effect. These results reflect laboratory based, non-sports related findings pointing to detrimental effects of sleep loss on executive function. 211
Towards quantitative metrics for architecture models

Software architectures and their representations in models are instrumental in achieving sustainability and the fulfillment of requirements. In this context, sustainability encompasses cost efficient maintainability and evolvability, which are central concerns for long living software systems. Hence, it is of great importance to support an architect in addressing these concerns when designing and evolving architectures. However, there is no framework available in which a designed architecture can be evaluated against these important quality attributes. In this paper, we address this challenge by proposing seven metrics which characterize the completeness, consistency, correctness and clarity of the documentation. These seven metrics should enable an architect to efficiently identify issues in an architecture model.
Genetic control of astrocyte function in neural circuits

During the last two decades numerous genetic approaches affecting cell function in vivo have been developed. Current state-of-the-art technology permits the selective switching of gene function in distinct cell populations within the complex organization of a given tissue parenchyma. The tamoxifen-inducible Cre/loxP gene recombination and the doxycycline-dependent modulation of gene expression are probably the most popular genetic paradigms. Here, we will review applications of these two strategies while focusing on the interactions of astrocytes and neurons in the central nervous system (CNS) and their impact for the whole organism. Abolishing glial sensing of neuronal activity by selective deletion of glial transmitter receptors demonstrated the impact of astrocytes for higher cognitive functions such as learning and memory, or the more basic body control of muscle coordination. Interestingly, also interfering with glial output, i.e., the release of gliotransmitters can drastically change animal’s physiology like sleeping behavior. Furthermore, such genetic approaches have also been used to restore astrocyte function. In these studies two alternatives were employed to achieve proper genetic targeting of astrocytes: transgenes using the promoter of the human glial fibrillary acidic protein (GFAP) or homologous recombination into the glutamate-aspartate transporter (GLAST) locus. We will highlight their specific properties that could be relevant for their use.
Photonic Crystal based sensor for sensing the salinity of seawater

A homogeneous, intensity modulated salinity sensor using Photonic Crystal Ring Resonator (PCRR) is proposed and designed for monitoring the salinity of seawater from 0 to 40% (0 to 40g/L) over the temperature between 0 to 25°C. The capability of the proposed sensor for sensing the salinity between 0 - 40% is theoretically examined. The sensor is composed of periodic Si rods embedded in an air host and a circular PCRR that is placed between the inline quasi waveguides. The concentration of salinity in seawater, changes the refractive index of the seawater. The change in refractive index of the seawater changes the output signal intensity of the sensor as seawater flowing insider the sensor. By detecting the output power and mapping to the salinity level, the salinity can be evaluated. Approximately, 2.69% of output power reduction is observed for every increasing 5% (5g/L) of salinity as the seawater has a unique refractive index for each salt level. With this underlying principle, the performance of the sensor is analyzed for different temperature.
Extraposition: A Case Study in German Sentence Realization

We profile the occurrence of clausal extraposition in corpora from different domains and demonstrate that extraposition is a pervasive phenomenon in German that must be addressed in German sentence realization. We present two different approaches to the modeling of extraposition, both based on machine learned decision tree classifiers. The two approaches differ in their view of the movement operation: one approach models multi-step movement through intermediate nodes to the ultimate target node, while the other approach models one-step movement to the target node. We compare the resulting models, trained on data from two domains and discuss the differences between the two types of models and between the results obtained in the different domains.
What are multi-protocol guessing attacks and how to prevent them

A guessing attack on a security protocol is an attack where an attacker guesses a poorly chosen secret (usually a low-entropy user password) and then seeks to verify that guess using other information. Past efforts to address guessing attacks in terms of design or analysis considered only protocols executed in isolation. However, security protocols are rarely executed in isolation and reality is always a case of mixed-protocols. In this paper, we introduce new types of attacks called multi-protocol guessing attacks, which can exist when protocols are mixed. We develop a systematic procedure to analyze protocols subject to guessing attacks and use this procedure to derive some syntactic conditions to be followed, in order for a protocol to be secure against multi-protocol guessing attacks. We then use the strand space framework to prove that a protocol will remain secure, given that these conditions are followed, by modeling the conditions within the framework. We illustrate these concepts using the Mellovin and Berritt protocol (EKE) as an example.
Structural Health Monitoring using Adaptive LMS Filters

A structure's level of damage is determined using a non-linear model-based method utilizing a Bouc-Wen hysteretic model. It employs adaptive least mean squares (LMS) filtering theory in real time to identify changes in stiffness due to modeling error damage, as well as permanent displacements, which are critical to determining ongoing safety and use. The structural health monitoring (SHM) method is validated on a 4-story shear structure model undergoing seismic excitation with 10% uniform noise added. The method identifies stiffness changes within 0.5-1.0% inside 0.2-1.0 seconds at different sampling frequencies. Permanent deflections are identified to within 10% of the true value in 1.0 second, converging further over the remainder of the record.