Miracle-dz/UniFAR-FTUs huggingface dataset:
Lymphoproliferative disorders in Oxford renal transplant recipients

Background: Increased cancer incidence, particularly lymphoproliferative disease, is a complication of immunosuppression in organ transplantation. Non-Hodgkin’s lymphomas (NHLs) occur frequently during the first year after transplantation, more so in North America than in Europe. Methods: This study audited and correlated the demographic, clinical, pathological, and outcome features of post-transplant lymphoproliferative disorders (PTLDs) in a large centre in Oxford, and assessed whether the time of onset fitted more with the European or North American pattern. Results: There were 1383 renal transplants in the study period and 27 patients developed lymphoma: 26 NHLs and one Hodgkin’s disease (1.95%). Four of the patients never received cyclosporin. The mean time of diagnosis after transplant was 46 months. Most tumours (21/27) presented extranodally. Management included reduction of immunosuppression, surgical excision, antiviral treatment, radiotherapy, and chemotherapy. Three patients presented in the first post-transplant year—0.34% of cyclosporin managed patients—similar to the North American incidence, although the incidence of extranodal late PTLDs was also high (mean onset, 36 months v 15 months international mean). Post-transplant lymphomas were the most common malignancy associated with death in transplant patients. Conclusions: PTLDs occurred in 2% of renal transplant patients, presenting both in the first year in association with cyclosporin use, as in North America, but also in subsequent years, giving an overall presentation time later than the international mean. The disease usually presented extranodally, accounting for the wide range of symptoms and signs. Despite awareness and active management, the disease contributed to death in more that 50% of patients with PTLDs.
Manifold learning combining imaging with non-imaging information

Recent work suggests that the space of brain magnetic resonance (MR) images can be described by a nonlinear and low-dimensional manifold. In the context of classifying Alzheimer's disease (AD) patients from healthy controls, we propose a method to incorporate subject meta-information into the manifold learning step. Information such as gender, age or genotype is often available in clinical studies and can inform the classification of a given query subject. In the proposed method, such information, whether discrete or continuous, can be used as an additional input to manifold learning and to enrich a distance measure derived from pairwise image similarities. Building on previous work, the Laplacian eigenmap objective function is extended to include the additional information. We use the ApoE genotype, the CSF-concentration of Aβ42 and hippocampal volume as meta-information to achieve significantly improved classification results for subjects in the Alzheimer's Disease Neuroimaging Initiative (ADNI) database.
STRESS TESTING A SUPPLY CHAIN USING SIMULATION

Simulation provides the capability to evaluate performance of a system operating under current or proposed configurations, policies and procedures. It is very applicable to evaluation of strategic and operational level plans for supply chains. It is especially useful for exploring the viability of a supply chain before beginning production. This paper describes the use of simulation for determining the readiness of a supply chain designed by a small company for providing sub-systems to a defense contractor. The supply chain had to be stress tested at surge and mobilization volume levels to meet the requirements. Simulation provided the ideal methodology to identify and demonstrate the behavior of the supply chain under stress and evaluate strategies to meet the defined volumes. It was used to prove the readiness of the supply chain reducing perceived risks in using the virtual operation.
Clinical implementation of hyperthermia treatment planning guided steering: A cross over trial to assess its current contribution to treatment quality

Purpose: To assess the current feasibility of online hyperthermia treatment planning guided steering (HGS) and its current contribution to treatment quality in deep hyperthermia for locally advanced cervical cancer. Materials and methods: 36 patients were randomized to receive either their second and fourth (arm A) or their third and fifth (arm B) hyperthermia treatment of the series with the aid of HGS. The other treatments were conducted according to the Rotterdam Empirical Steering Guidelines (RESG). Results: During period I (second and third treatment of the series) similar results were found for HGS and RESG with a slight, non-significant difference found in favour of HGS. The average temperature T50 was 40.3°C for both (p = 0.409) and the dose parameter CEM43T90 was 0.64 for RESG and 0.63 for HGS (p = 0.154). However, during period II (fourth and fifth treatment of the series) HGS performed less well, with significant lower thermal dose parameters, minimum, mean and maximum intraluminal temperatures, tolerance measures and net integrated power. T50 was 40.4°C after RESG and 40°C after HGS (p = 0.001) and CEM43T90 0.57 and 0.38 (p = 0.01) respectively. Conclusion: We found that the procedure of online treatment planning guided steering is feasible. For maximal exploitation of its possibilities, however, better control and understanding of several patient, tumour and technical parameters is required. This study has been very helpful in identifying some of the challenges and flaws that warrant further investigation in the near future, such as patient positioning and the prevention of hotspot-related complaints.
The Labeled Segmentation of Printed Books

We introduce the task of book structure labeling: segmenting and assigning a fixed category (such as Table of Contents, Preface, Index) to the document structure of printed books. We manually annotate the page-level structural categories for a large dataset totaling 294,816 pages in 1,055 books evenly sampled from 1750-1922, and present empirical results comparing the performance of several classes of models. The best-performing model, a bidirectional LSTM with rich features, achieves an overall accuracy of 95.8 and a class-balanced macro F-score of 71.4.
Differential expression of molecular markers of synaptic plasticity in the hippocampus, prefrontal cortex, and amygdala in response to spatial learning, predator exposure, and stress‐induced amnesia

We have studied the effects of spatial learning and predator stress‐induced amnesia on the expression of calcium/calmodulin‐dependent protein kinase II (CaMKII), brain‐derived neurotrophic factor (BDNF) and calcineurin in the hippocampus, basolateral amygdala (BLA), and medial prefrontal cortex (mPFC). Adult male rats were given a single training session in the radial‐arm water maze (RAWM) composed of 12 trials followed by a 30‐min delay period, during which rats were either returned to their home cages or given inescapable exposure to a cat. Immediately following the 30‐min delay period, the rats were given a single test trial in the RAWM to assess their memory for the hidden platform location. Under control (no stress) conditions, rats exhibited intact spatial memory and an increase in phosphorylated CaMKII (p‐CaMKII), total CaMKII, and BDNF in dorsal CA1. Under stress conditions, rats exhibited impaired spatial memory and a suppression of all measured markers of molecular plasticity in dorsal CA1. The molecular profiles observed in the BLA, mPFC, and ventral CA1 were markedly different from those observed in dorsal CA1. Stress exposure increased p‐CaMKII in the BLA, decreased p‐CaMKII in the mPFC, and had no effect on any of the markers of molecular plasticity in ventral CA1. These findings provide novel observations regarding rapidly induced changes in the expression of molecular plasticity in response to spatial learning, predator exposure, and stress‐induced amnesia in brainregions involved in different aspects of memory processing. © 2011 Wiley Periodicals, Inc.
Catadioptric Stereo For Robot Localization

Stereo rigs are indispensable in real world 3D localization and reconstruction, yet they are costly and the additional camera adds complexity. Catadioptric systems offer an inexpensive alternative, with the bonus of being taken from the same camera. I explore the design and calibration of such a rig, and begin to evaluate its utility for robot localization.
Assessing the need for sequence-based normalization in tiling microarray experiments

MOTIVATION Increases in microarray feature density allow the construction of so-called tiling microarrays. These arrays, or sets of arrays, contain probes targeting regions of sequenced genomes at regular genomic intervals. The unbiased nature of this approach allows for the identification of novel transcribed sequences, the localization of transcription factor binding sites (ChIP-chip), and high resolution comparative genomic hybridization, among other uses. These applications are quickly growing in popularity as tiling microarrays become more affordable. To reach maximum utility, the tiling microarray platform needs be developed to the point that 1 nt resolutions are achieved and that we have confidence in individual measurements taken at this fine of resolution. Any biases in tiling array signals must be systematically removed to achieve this goal. RESULTS Towards this end, we investigated the importance of probe sequence composition on the efficacy of tiling microarrays for identifying novel transcription and transcription factor binding sites. We found that intensities are highly sequence dependent and can greatly influence results. We developed three metrics for assessing this sequence dependence and use them in evaluating existing sequence-based normalizations from the tiling microarray literature. In addition, we applied three new techniques for addressing this problem; one method, adapted from similar work on GeneChip brand microarrays, is based on modeling array signal as a linear function of probe sequence, the second method extends this approach by iterative weighting and re-fitting of the model, and the third technique extrapolates the popular quantile normalization algorithm for between-array normalization to probe sequence space. These three methods perform favorably to existing strategies, based on the metrics defined here. AVAILABILITY http://tiling.gersteinlab. org/sequence_effects/
Effects of acetazolamide on proximal tubule C1, Na, and HCO3 transport in normal and acidotic dogs during distal blockade.

It has been suggested that the establishment of a tubular fluid to plasma chloride gradient in the late proximal tubule by the reabsorption of bicarbonate (and other anions) in the early proximal tubule is responsible for a significant part of sodium chloride and water reabsorption in the proximal tubule. In the present study the effects of acetazolamide on proximal tubule water and electrolyte excretion were examined in 6 normal dogs and 10 chronic ammonium chloride-loaded dogs during distal blockade produced by ethacrynic acid and chlorothiazide administration. During distal blockade control urine/plasma osmolality and urine/plasma sodium were close to unity in all experiments. Urine/plasma chloride and urine/plasma bicarbonate were 1.21+/-0.02 and 0.75+/-0.07 in normal and 1.24+/-0.01 and 0.04+/-0.01 in acidotic dogs, respectively. After the administration of acetazolamide (20 mg/kg i.v.), there was a significant increase in urine flow, absolute and fractional excretion of sodium, bicarbonate, and chloride in all animals. Associated with these effects, urine/plasma osmolality and urine/plasma sodium remained unchanged but urine/plasma chloride decreased significantly to 1.15+/-0.01 in normal and to 1.19+/-0.01 in acidotic dogs. In acidotic dogs there was a significant correlation between the increase in bicarbonate, sodium, or chloride excretion after acetazolamide and the plasma bicarbonate level (range 6.8-12.5 meq/liter). These data demonstrate a significant effect of acetazolamide on bicarbonate, sodium, and chloride reabsorption in the proximal tubule even in the face of severe acidosis. Moreover, the data suggest that the decrease in chloride reabsorption (and accompanying sodium) after acetazolamide is related to the decrease in bicarbonate reabsorption and the associated decrease in the transtubular chloride gradient.
Statistical Applications in Genetics and Molecular Biology Granger Causality Analysis of Human Cell-Cycle Gene Expression Profiles

Granger causality (GC) tests are ideally suited to investigate time series data generated by bivariate vector autoregressive (VAR) processes. Recent studies have applied GC analysis and its extensions for modeling functional relationships and network structure from temporal gene expression profiles. The present study investigates GC analysis of human cell-cycle gene expression profiles that can be modeled as a first-order bivariate VAR. Analytical results presented establish the contribution of the VAR process parameters, including auto-regulatory feedback and noise variance to the mean-squared forecast error, as a critical component in identifying statistically significant GC relationships. These results in turn discourage blind inference of functional relationship between a given pair of genes solely based on the result of the statistical tests for GC. The presence of significant auto-regulatory feedback and discrepancy in noise variance is demonstrated across the cell-cycle gene expression profiles by VAR parameter estimation. It is emphasized that discrepancies in noise variance can be due to artifacts and can lead to spurious existence of functional relationship between a given pair of genes. VAR parameter estimation is encouraged for better of GC interpretation of the results. Published case studies on GC analysis of the same publicly available cell-cycle gene expression data are reinvestigated for transparency.
Quality of life of Elderly Diabetic and Hypertensive People – Impact of Intervention Programme

A research project was conducted to study the quality of life (QoL) of elderly diabetic and hypertensive people in Bangalore city. The objective of the study was to evaluate an educational module developed to help the elderly to cope with prevailing conditions and improve their quality of life. The sample consisted of 80 elderly of which 40 were men and 40 were women between the age group 65 to 76 years. The QoL was assessed through the standardized scale WHO –QoL-100 felid version. A quasi experimental approach with a repeated measure design was used with provision to compare the pre and post intervention assessment for the evaluation of the non-formal educational module for its effectiveness in improving the knowledge and quality of life of the elderly. The ‘t’ test was applied to see the significance of differences in the mean scores of men and women and the two age groups as well as the pre and post intervention assessments. The findings revealed that the post test scores on the overall QOL were higher than the pre test scores and the individual differences in the scores were also reduced considerably during post test for men and women as well as the two age groups. Statistically significant gain was noticed on all the five domains of QOL after the intervention
Numerical homogenization of nonlinear viscoplastic two-dimensional polycrystals

In this article, we numerically determine the effective stress-strain relation of some two-dimensional polycrystals. These are aggregates of a few tens of perfectly bonded single-crystal (hexagonal atomic lattice) grains, with varying orientations. Each grain obeys a given nonlinear viscoplastic stress-strain relation, which depends on the orientation of the grain. Precise calculations performed with this microscopic model are compared with calculations done with a macroscopic approximate model (in which matter has no microstructure) in order to determine the macroscopic constitutive law. We find an effective behaviour for the stationary response which appears to be also consistent for the transient response. The influence of the number of grains as well as that of the distribution of grain orientations are investigated.
Directional asymmetries in human smooth pursuit eye movements.

PURPOSE Humans make smooth pursuit eye movements to bring the image of a moving object onto the fovea. Although pursuit accuracy is critical to prevent motion blur, the eye often falls behind the target. Previous studies suggest that pursuit accuracy differs between motion directions. Here, we systematically assess asymmetries in smooth pursuit. METHODS In experiment 1, binocular eye movements were recorded while observers (n = 20) tracked a small spot of light moving along one of four cardinal or diagonal axes across a featureless background. We analyzed pursuit latency, acceleration, peak velocity, gain, and catch-up saccade latency, number, and amplitude. In experiment 2 (n = 22), we examined the effects of spatial location and constrained stimulus motion within the upper or lower visual field. RESULTS Pursuit was significantly faster (higher acceleration, peak velocity, and gain) and smoother (fewer and later catch-up saccades) in response to downward versus upward motion in both the upper and the lower visual fields. Pursuit was also more accurate and smoother in response to horizontal versus vertical motion. CONCLUSIONS. Our study is the first to report a consistent up-down asymmetry in human adults, regardless of visual field. Our findings suggest that pursuit asymmetries are adaptive responses to the requirements of the visual context: preferred motion directions (horizontal and downward) are more critical to our survival than nonpreferred ones.
Hop-by-Hop Congestion Control Over a Wireless Multi-Hop Network

This paper focuses on congestion control over multi-hop, wireless networks. In a wireless network, an important constraint that arises is that due to the MAC (Media Access Control) layer. Many wireless MACs use a time-division strategy for channel access, where, at any point in space, the physical channel can be accessed by a single user at each instant of time. In this paper, we develop a fair hop-by-hop congestion control algorithm with the MAC constraint being imposed in the form of a channel access time constraint, using an optimization-based framework. In the absence of delay, we show that this algorithm are globally stable using a Lyapunov-function-based approach. Next, in the presence of delay, we show that the hop-by-hop control algorithm has the property of spatial spreading. In other words, focused loads at a particular spatial location in the network get "smoothed" over space. We derive bounds on the "peak load" at a node, both with hop-by-hop control, as well as with end-to-end control, show that significant gains are to be had with the hop-by-hop scheme, and validate the analytical results with simulation
Has potassium been prematurely discarded as a contributing factor to the development of uraemic neuropathy?

Sobell Department of Neurophysiology, Institute of Neurology and Department of Clinical Neurophysiology, National Hospital for Neurology and Neurosurgery, London, Department of Renal Medicine, St Mary’s Hospital, London, UK, Department of Clinical Neurophysiology, Glostrup Hospital, University of Copenhagen, Glostrup, Denmark, Prince of Wales Medical Research Institute, University of New South Wales and the Institute of Neurological Sciences, Prince of Wales Hospital, Sydney, Australia
Micropropagation of Anthurium spp.

Micropropagation as an alternative method to conventional propagation, the culture of somatic cells, tissues and organs of plants under controlled conditions is a suitable way to produce a large number of progeny plants which are genetically identical to the stock plant in a short time. The important property of the plant cells is totipotency which is a capacity to produce the whole plant from different plant parts. Micropropagation has some features to be chosen in commercial production such as multiplicative capacity in a relatively short time, healthy and disease-free production capacity and ability to generate population during a year [1-5].
Microfluidics – ALab in Your Palm

(right) Sajan D George is an Associate Professor at Center for Atomic and Molecular Physics, Manipal University. India. His research interests include micro and optofluidics, nanophotonics, biomedical applications of laser and photothermal methods. A few decades ago electronics evolved from huge circuits based on vacuum tubes into small scale semiconducting integrated circuits. In simple words, a calculator that was as huge as a room, now ts into a wrist watch. Nowadays, a similar trend is observed in bio and chemical engineering. Analysis and synthesis involving °uids, which originally could be done only on large scales, are more and more integrated into small devices called micro°uidic chips. Such microsacle or even nanoscale devices, in general called labon-a-chip devices, o®er a higher accuracy and better e±ciency compared to bulk devices. In this article we describe some important aspects about micro°uidics.
Intelligent agents for retrieving chinese Web financial news

As the popularity of World Wide Web increases, many newspapers expand their services by providing news information on the Web in order to be competitive and increase benefit. The Web provides real time dissemination of financial news to investors. However, most investors find it difficult to search for the financial information of interest from the huge Web information space. Most of the commercial search engines are not user friendly and do not provide any tailor-made intelligent agents to search for relevant Web documents on behalf of users. Users have to exert a lot of effort to submit an appropriate query to obtain the information they want. Intelligent agents that learn user preferences and monitor the postings of Web information providers are desired. In this paper, we present an intelligent agent that utilizes user profiles and user feedback to search for the Chinese Web financial news articles on behalf of users. A Chinese indexing component is developed to index the continuously fetched Chinese financial news articles. User profiles capture the basic knowledge of user preferences based on the sources of news articles, the regions of the news reported, categories of industries related, the listed companies, and user specified keywords. User feedback captures the semantics of the user rated news articles. The search engine will rank the top 20 news articles that users are most interested in based on these inputs. Experiments were conducted to measure the performance of the agents based on the inputs from user profile and user feedback.