Miracle-dz/UniFAR-FTUs huggingface dataset:
Inferring input nonlinearities in neural encoding models

We describe a class of models that predict how the instantaneous firing rate of a neuron depends on a dynamic stimulus. The models utilize a learnt pointwise nonlinear transform of the stimulus, followed by a linear filter that acts on the sequence of transformed inputs. In one case, the nonlinear transform is the same at all filter lag-times. Thus, this “input nonlinearity” converts the initial numerical representation of stimulus value to a new representation that provides optimal input to the subsequent linear model. We describe algorithms that estimate both the input nonlinearity and the linear weights simultaneously; and present techniques to regularise and quantify uncertainty in the estimates. In a second approach, the model is generalized to allow a different nonlinear transform of the stimulus value at each lag-time. Although more general, this model is algorithmically more straightforward to fit. However, it has many more degrees of freedom than the first approach, thus requiring more data for accurate estimation. We test the feasibility of these methods on synthetic data, and on responses from a neuron in rodent barrel cortex. The models are shown to predict responses to novel data accurately, and to recover several important neuronal response properties.
Genetic variations in the serotonin 5-HT2A receptor gene (HTR2A) are associated with rheumatoid arthritis

Objectives: To analyse the association between the genetic polymorphisms within the HTR2A gene for the serotonin receptor and rheumatoid arthritis (RA). Methods: HTR2A gene polymorphisms were analysed in patients with RA and controls from two study populations using PCR based restriction endonuclease mapping or TaqMan allelic discrimination with more than 4000 individuals included in the current study. Results: At the discovery stage we detected significant differences in frequency of rs6313 (T102C polymorphism) between the patients with RA and controls (p = 0.006). Following validation with an extended set of single nucleotide polymorphisms (SNPs) and number of DNA samples, a trend in associations in allelic model for SNPs rs6314, rs1328674, rs6313 and rs6311 (p = 0.006, 0.002, 0.006, 0.009) was seen, although it was lost after correction for multi-comparison for all but rs1328674 (empirical p value = 0.021). However, haplotype frequency analysis based on these four SNPs showed significantly low representation of TCTT combination in patients with RA in comparison with controls (3.6% and 5.6%, p<0.001 on χ2 test, empirical p = 0.004 after 100 000 permutations) and a significantly higher frequency of CTCC combination in patients with RA in comparison with controls (3.6% and 2.2%, p = 0.002 on χ2 test, empirical p = 0.022 after 100 000 permutations). Conclusions: In our study, genetic polymorphisms at the HTR2A gene are associated with susceptibility for RA, suggesting possible links between the serotonergic system and development of the disease.
Performance Analysis of CNTs as an Application for Future VLSI Interconnects

This paper presents performance evaluation of different types of carbon-nanotubes(CNTs) based interconnects viz. Single-walled carbon nanotubes(SWCNT), Bundle SWCNT(B-SWCNT), Multiwalled CNT(M-WCNT) as well as Copper interconnects. The CNT-metal contact resistance has been taken into consideration in the model used in this work. In case of copper interconnects the effect of surface scattering and grain boundary scattering is accounted for. The effect of change in B-SWCNT packaging density on performance of B-SWCNT is analyzed for the first time. A method is proposed to find out the packaging density of a symmetric B-SWCNT structure. SPICE simulations verify the results for 45nm technology node.
Robotic system for single incision laparoscopic surgery

This paper proposes a robotic system to assist and collaborate with surgeons in Single Incision Laparoscopic Surgery (SILS) operations. The system, aim at solving the main drawbacks of this kind of surgery, is composed of a miniature camera robot and a redundant robotic grasper. Positioning of both robots inside the patient's abdomen is done by means of magnetic control. External magnetic sources are placed at the end effector of two robotic arms, and permanent magnets are integrated in the robots. Camera robot is provided with three permanent magnets, so both position and orientation can be controlled. Sliding control, which is robust against perturbations and parameter uncertainties, is chosen. Robotic grasper's redundancy makes possible autonomously obstacle avoidance and increases its workspace. The haptic device is designed so as surgeons can handle the grasper as if it were a conventional tool. In order to this aim, augmented reality is used to simulate a traditional tool in the visual feedback system, in substitution of the robotic grasper. Besides the telemanipulation, requirements for autonomously functions to assist surgeons in the specific tasks of suturing are discussed.
Blocking artifacts removal by a hybrid filter method

Blocking artifacts are the visual artifacts found at block boundaries of DCT-based compressed images. The blocking artifacts removal method in this paper simultaneously performs an edge-preserving and a low-pass ﬁltering of the degraded image. The de-blocked result is then constructed from a soft blending of the two ﬁltered outputs. The novel contribution here is the soft blending that avoids hard segmentation of the image into monotone and textured regions, thereby eliminating boundary artifacts after segment uniﬁcation. The 1-dimensional oriented ﬁlter is an ef-ﬁcient adaptive ﬁlter that enhances lines and edges for textured regions. Results from experiments show that the proposed algorithm signiﬁcantly reduces artifacts of compressed images from a wide bit-rate range in a reasonably short amount of time.
Genetic Variation within the Mx Gene of Commercially Selected Chicken Lines Reveals Multiple Haplotypes, Recombination and a Protein under Selection Pressure

The Mx protein is one of the best-characterized interferon-stimulated antiviral mediators. Mx homologs have been identified in most vertebrates examined; however, their location within the cell, their level of activity, and the viruses they inhibit vary widely. Recent studies have demonstrated multiple Mx alleles in chickens and some reports have suggested a specific variant (S631N) within exon 14 confers antiviral activity. In the current study, the complete genome of nine elite egg-layer type lines were sequenced and multiple variants of the Mx gene identified. Within the coding region and upstream putative promoter region 36 SNP variants were identified, producing a total of 12 unique haplotypes. Each elite line contained from one to four haplotypes, with many of these haplotypes being found in only one line. Observation of changes in haplotype frequency over generations, as well as recombination, suggested some unknown selection pressure on the Mx gene. Trait association analysis with either individual SNP or haplotypes showed a significant effect of Mx haplotype on several egg production related traits, and on mortality following Marek's disease virus challenge in some lines. Examination of the location of the various SNP within the protein suggests synonymous SNP tend to be found within structural or enzymatic regions of the protein, while non-synonymous SNP are located in less well defined regions. The putative resistance variant N631 was found in five of the 12 haplotypes with an overall frequency of 47% across the nine lines. Two Mx recombinants were identified within the elite populations, indicating that novel variation can arise and be maintained within intensively selected lines. Collectively, these results suggest the conflicting reports in the literature describing the impact of the different SNP on chicken Mx function may be due to the varying context of haplotypes present in the populations studied.
Design of multimedia semantic presentation templates: options, problems and criteria of use

This paper presents and discusses the use of Semantic Multimedia Presentation Templates which capture presentation structures that are suitable for communicating semantic data relationships occurring across many applications. The identification of the space of the possible presentation templates along with criteria to evaluate them that depend on the current task, data cardinality and other aspects, is very useful for supporting the automatic generation of effective query result multimedia presentations.
Domain adaptation using maximum likelihood linear transformation for PLDA-based speaker verification

While i-vector-PLDA frameworks employing huge amounts of development data have achieved significant success in speaker recognition, it is infeasible to collect a sufficiently large amount of data for every real application. This paper proposes a method to perform supervised domain adaptation of PLDA in i-vector-based speaker recognition systems with available resource-rich mismatched data and small amounts of matched data, under two assumptions: (1) between-speaker and within-speaker covariances depend on domains; (2) features in one domain can be transformed into another domain by means of an affine transformation. Maximum likelihood linear transformation (MLLT) is used to infer the relationship between the datasets of two domains in training PLDA. The proposed method improves performance over that achieved without adaptation. Using a score fusion technique, it outperforms a conventional method based on linear combination.
Ru Alloy-Oxide Buffer Layer for Intergranular Exchange Decoupling of CoPt–B2O3 Granular Media

Investigation of magnetic properties and microstructure for the Co<sub>80</sub>Pt<sub>20</sub>–30vol% B<sub>2</sub>O<sub>3</sub> granular medium to clarify the effect of utilizing buffer layer (BL) on intergranular exchange coupling was conducted. It was found that the employment of a Ru<sub>50</sub>Co<sub>25</sub>Cr<sub>25</sub>–30vol% TiO<sub>2</sub> BL with thickness of around 2 nm will avoid physical contact between magnetic grains in the initial growth region, which is effective to intergranular exchange decouple the magnetic grains. On the other hand, for deposition of BL thicker than 2 nm, underlayer will be flatten that brings the possibility of physical contact of magnetic grains and forms a granular film with strong intergranular exchange coupling.
Analysis of Fibrous Composition for Hygienic Purpose – Recommendations for Application on Feminine Underwear

The vulva-vaginal infections are common in women. The textile materials, used in underwear and absorbent hygiene products, are identified as risk factors, but their influence on the emergence of these infections is not yet clear. Bacterial adhesion is associated with persistence of microorganisms in the material that is related to the recurrence of infections. This paper is an initial attempt for the elucidation of these questions. Some of the main features involved in this phenomenon are identified and characterized.
Word-based acoustic confidence measures for large-vocabulary speech recognition

Word level confidence measures are of use in many areas of speech recognition. Comparing the hypothesized word score to the score of a ‘filler’ model has been the most popular confidence measure because it is highly efficient, and does not require a large amount of training data. This paper explores an extension of this technique which also compares the hypothesized word score to the scores of words that are commonly confused for it, while maintaining efficiency and the low demand for training data. The proposed method gives a 39% relative false accept rate reduction over the ‘filler’model baseline, at a false reject rate of 5%.
Directed Evolution Generates a Novel Oncolytic Virus for the Treatment of Colon Cancer

Background Viral-mediated oncolysis is a novel cancer therapeutic approach with the potential to be more effective and less toxic than current therapies due to the agents selective growth and amplification in tumor cells. To date, these agents have been highly safe in patients but have generally fallen short of their expected therapeutic value as monotherapies. Consequently, new approaches to generating highly potent oncolytic viruses are needed. To address this need, we developed a new method that we term “Directed Evolution” for creating highly potent oncolytic viruses. Methodology/Principal Findings Taking the “Directed Evolution” approach, viral diversity was increased by pooling an array of serotypes, then passaging the pools under conditions that invite recombination between serotypes. These highly diverse viral pools were then placed under stringent directed selection to generate and identify highly potent agents. ColoAd1, a complex Ad3/Ad11p chimeric virus, was the initial oncolytic virus derived by this novel methodology. ColoAd1, the first described non-Ad5-based oncolytic Ad, is 2–3 logs more potent and selective than the parent serotypes or the most clinically advanced oncolytic Ad, ONYX-015, in vitro. ColoAd1's efficacy was further tested in vivo in a colon cancer liver metastasis xenograft model following intravenous injection and its ex vivo selectivity was demonstrated on surgically-derived human colorectal tumor tissues. Lastly, we demonstrated the ability to arm ColoAd1 with an exogenous gene establishing the potential to impact the treatment of cancer on multiple levels from a single agent. Conclusions/Significance Using the “Directed Evolution” methodology, we have generated ColoAd1, a novel chimeric oncolytic virus. In vitro, this virus demonstrated a >2 log increase in both potency and selectivity when compared to ONYX-015 on colon cancer cells. These results were further supported by in vivo and ex vivo studies. Furthermore, these results have validated this methodology as a new general approach for deriving clinically-relevant, highly potent anti-cancer virotherapies.
A comparison of iron absorption in adults and infants consuming identical infant formulas

Fe absorption was estimated in adults and infants from the erythrocyte incorporation of Fe isotopes added to infant formula. Fe absorption was measured in adults using radioisotopes, and in infants with a stable-isotope technique. In adults, the geometric mean Fe absorption from a ready-to-feed soya formula with its native phytic acid content was 2·4%. This increased to 6·0% (P < 0·05) after almost complete dephytinization. In infants, mean Fe absorption values were 3·9 and 8·7% respectively from the same products (P <0·05). In adults, mean Fe absorption from a spray-dried soya formula containing 110mg ascorbic acid/I was 4·1%, increasing to 5·3% (P < 0·05) when ascorbic acid was doubled to 220 mg/l. In infants, mean Fe absorption values were 5·7 and 9·5% (P < 0·05) from the same products. Mean Fe absorption from a milk-based formula was 6·5% in adults compared with 6·7% in infants. All meals in the adult and infant studies were fed using an identical meal size of 217g. Increasing the meal size threefold in adults did not change fractional Fe absorption. Mean Fe absorption values for each meal were lower in adults than in infants, but the relative inhibitory effect of phytic acid and the enhancing effect of ascorbic acid were similar. We conclude that Fe absorption studies in adults can be used to assess the influence of enhancers and inhibitors of Fe absorption in infant formulas fed to infants. Further studies, however, are required to extend these findings to weaning foods and complete meals.
Effect of Postoperative Epidural Analgesia on Rehabilitation and Pain after Hip Fracture Surgery: A Randomized, Double-blind, Placebo-controlled Trial

Background:Hip fracture surgery usually carries a high demand for rehabilitation and a significant risk of perioperative morbidity and mortality. Postoperative epidural analgesia may reduce morbidity and has been shown to facilitate rehabilitation in elective orthopedic procedures. No studies exist on the effect of postoperative epidural analgesia on pain and rehabilitation after hip fracture surgery. Methods:Sixty elderly patients were included in a randomized, double-blind study comparing 4 days of continuous postoperative epidural infusion of 4 ml/h bupivacaine, 0.125%, and 50 &mgr;g/ml morphine versus placebo. Both patient groups received balanced analgesia and intravenous nurse-controlled analgesia with morphine. All patients followed a well-defined multimodal rehabilitation program. Pain, ability to participate in four basic physical functions, and any factors restricting participation were assessed on the first 4 postoperative days during physiotherapy. Results:Epidural analgesia provided superior dynamic analgesia during all basic physical functions, and patients were significantly less restricted by pain, which was the dominating restricting factor in the placebo group. Motor blockade was not a restricting factor during epidural analgesia. Despite improved pain relief, scores for recovery of physical independence were not different between groups. Conclusion:Postoperative epidural analgesia after hip fracture surgery provides superior analgesia attenuating pain as a restricting factor during rehabilitation without motor dysfunction. However, superior analgesia did not translate into enhanced rehabilitation. Future studies with multimodal rehabilitation are required to establish whether superior analgesia can be translated into enhanced rehabilitation and reduced morbidity in hip fracture patients.
of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Ehrlichia chaffeensis: a Prototypical Emerging Pathogen Ehrlichia chaffeensis: a Prototypical Emerging Pathogen

Infected nymphs may transmit E. chaffeensis to susceptible reservoir hosts (unshaded) or to humans during acquisition of blood. Infected adult ticks, having acquired ehrlichiae either by transstadial transmission from infected nymphal stage or during blood meal acquisition as noninfected nymphs on infected deer, may also pass E. chaffeensis to humans or other susceptible reservoirs. Transovarial transmission has not been demonstrated, and eggs and unfed larvae are presumably not infected.
Support system for novice researchers (ssnr): usability evaluation of the first use

Scholars make use of research output in the form of conference proceedings, journal and theses as references as guideline in generating new knowledge for the use of future generations. Support in the early stage of study is crucial for novice researchers as it will give them some insights of where to seek for extra information on relevant literature, institutions, people and research trend without having to go through tedious process of identifying this information all by themselves. The result of the implementation of SSNR shows significant information that can be utilized by novice researchers in accelerating research process. Thus, this paper will discuss on the evaluation of SSNR by novice researchers, in terms of its usability. The results are promising which indicated that SSNR work as it should .
OCR-aided person annotation and label propagation for speaker modeling in TV shows

In this paper, we present an approach for minimizing human effort in manual speaker annotation. Label propagation is used at each iteration of an active learning cycle. More precisely, a selection strategy for choosing the most suitable speech track to be labeled is proposed. Four different selection strategies are evaluated and all the tracks in a corresponding cluster are gathered using agglomerative clustering in order to propagate human annotations. To further reduce the manual labor required, an optical character recognition system is used to bootstrap annotations. At each step of the cycle, annotations are used to build speaker models. The quality of the generated speaker models is evaluated at each step using an i-vector based speaker identification system. The presented approach shows promising results on the REPERE corpus with a minimum amount of human effort for annotation.
Experimental Testing of Materials Used in Fused Deposition Modeling Rapid Prototyping Technology

In this paper are presented information about common and advanced materials used for manufacturing of products by Fused Deposition Modelling (FDM) rapid prototyping technology. In different rapid prototyping technologies the initial state of material can come in either solid, liquid or powder state. The current range materials include paper, nylon, wax, resins, metals and ceramics. In FDM are mainly used as basic materials ABS - Acrylonitrile Butadiene Styrene, polyamide, polycarbonate, polyethylene and polypropylene. Main part of the paper is focused on experimental testing of rapid prototyping materials realized by different research teams and presents outputs of testing of ABS material in FDM technology realized by authors.
Serum n-3 and n-6 polyunsaturated fatty acid profile as an independent predictor of cardiovascular events in hemodialysis patients.

BACKGROUND Unlike the n-6 polyunsaturated fatty acid (PUFA) arachidonic acid (AA), n-3-PUFAs such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) appear to have beneficial effects on inflammation, thrombosis, and cardiovascular disease (CVD). We examined possible alterations in serum PUFA profiles in patients on maintenance hemodialysis therapy and its association with CVD risk. STUDY DESIGN An observational study including cross-sectional and longitudinal analyses. SETTING & PARTICIPANTS Single-center study of 517 maintenance hemodialysis patients in an urban area in Japan. PREDICTORS Serum EPA, DHA, and AA concentrations and EPA:AA, DHA:AA, and (EPA+DHA):AA ratios. OUTCOMES CVD events, including ischemic heart disease, stroke, peripheral artery disease, pulmonary edema, and valve disease. RESULTS Hemodialysis patients showed lower (EPA+DHA):AA, EPA:AA, and DHA:AA ratios than 122 controls similar in age and sex. During follow-up, 190 CVD events were recorded. (EPA+DHA):AA ratio was not associated significantly with CVD in unadjusted analysis, but was associated significantly and inversely with CVD in Cox models adjusted for age and other confounding variables, with HRs in the range of 1.71-1.99 in the lowest versus highest quartile of (EPA+DHA):AA ratios. Similarly, EPA:AA and DHA:AA ratios showed inverse associations with CVD, whereas serum EPA, DHA, and AA concentrations were not predictive of CVD. LIMITATIONS No information for dietary intake, use of dietary supplements, or cell membrane PUFA content. CONCLUSIONS In hemodialysis patients, serum PUFA profile is unfavorably altered, and the low n-3-PUFA:AA ratios are independent predictors of CVD.