Miracle-dz/UniFAR-FTUs huggingface dataset:
A major quantitative trait locus for increasing cadmium-specific concentration in rice grain is located on the short arm of chromosome 7

Large phenotypic variations in the cadmium (Cd) concentration of rice grains and shoots have been observed. However, the genetic control of Cd accumulation remains poorly understood. Quantitative trait loci (QTLs) determining the grain Cd concentration of rice grown in a Cd-polluted paddy field were identified. Using a mapping population consisting of 85 backcross inbred lines derived from a cross between the low-Cd-accumulating cultivar Sasanishiki (japonica) and high-Cd-accumulating cultivar Habataki (indica), two QTLs for increasing grain Cd concentration were found on chromosomes 2 and 7. A major-effect QTL, qGCd7 (QTL for grain Cd on chromosome 7), was detected on the short arm of chromosome 7. It accounted for 35.5% of all phenotypic variance in backcross inbred lines. qGCd7 was not genetically related to any QTLs for concentrations of essential trace metals (Cu, Fe, Mn, and Zn) or those for agronomic traits such as heading date, suggesting that this QTL is specific to Cd. Furthermore, the existence of qGCd7 was confirmed using chromosome segment substitution lines (CSSLs) and an F2 population from a cross between the target CSSL and Sasanishiki grown in a Cd-polluted paddy soil. To our knowledge, qGCd7 is a novel QTL with major effects for increasing grain Cd concentrations.
Baroreflex and Vagal Mechanisms Modulating Left Ventricular Contractile Responses to Sympathomimetic Amines in Conscious Dogs

The steady state effects of intravenous norepinephrine (NE), 0.2 7μg/kg per min, isoproterenoL 0.02 pg/kg per min, and dopamine, 10 pg/kg per min, on measurements of arterial and left ventricular (LV) pressures, dP/dt, LV diameter, and velocity of shortening were compared before and after muscarinic blockade with atropine sulfate or methyl atropine bromide (0.1 mg/kg). In intact conscious dogs, NE increased mean arterial pressure by 24 ± 2 mm Hg and LV dP/dt by 1140 ± 90 mm Hg/sec, but did not change LV velocity significantly and decreased heart rate by 13 ± 3 beats/min. After muscarinic blockade, NE caused significantly greater (P < 0.01) increases in mean arterial pressure of 49 ± 6 mm Hg, LV dP/dt of 3290 ± 240 mm Hg/sec, LV velocity of 24 mm/sec, and heart rate of 7 ± 3 beats/min. A similar augmentation of the contractile response to infusions of isoproterenol and dopamine was observed following muscarinic blockade. These responses were dependent neither on arterial baroreceptors nor on an intact sympathetic nervous system. After vagotomy and arterial baroreceptor denervation (ABD), NE increased LV dP/dt by 2970 ± 170 mm Hg/sec and LV velocity by 20 ± 4 mm/sec, i.e., by amounts similar to those found after muscarinic blockade for intact dogs and dogs with ABD. However, in dogs with ABD and vagotomy, the contractile responses to NE were not augmented further by muscarinic blockade. Thus, the parasympathetic nervous system can exert a powerful inhibitory influence on the inotropic responses to infused sympathomimetic amines since, after muscarinic blockade, the inotropic responses to NE, isoproterenol, and dopamine increase 2-fold. The mechanism is independent of the arterial baroreceptor reflex and the sympathetic nervous system and appears to involve an inhibitory action of vagally released acetylcholine on the β-adrenergic inotropic response to sympathomimetic amines. Ore Res 44:195-207, 1979
Biases in differential expression analysis of RNA-seq data: A matter of replicate type

In differential expression (DE) analysis of RNA-seq count data, it is known that genes with a larger read number are more likely to be differentially expressed. This bias has a profound effect on the subsequent Gene Ontology (GO) analysis by perturbing the ranks of gene-sets. Another known bias is that the commonly used parametric DE analysis methods (e.g., edgeR, DESeq and baySeq) tend to yield more DE genes as the sequencing depth is increased. We nevertheless show that these biases are in fact confined to data of the technical replicate type. We also show the GO or gene-set enrichment analysis methods applied to technical replicate data result in considerable number of false positives. In conclusion, the current DE and enrichment analysis methods can be confidently used for biological replicate count data, while caution should be exercised when analysing technical replicate data.
Economic impact of delaying or preventing AIDS in persons with HIV.

OBJECTIVES To investigate how preventing or delaying the development of acquired immune deficiency syndrome (AIDS) [or other severe conditions related to the human immunodeficiency virus (HIV)] through antiretroviral therapy affects the lifetime cost of HIV/AIDS care, and to compare the cost of therapy with the potential savings in HIV/AIDS-related end-of-life care. METHODS The analysis utilized a previously developed economic model of HIV/AIDS-related medical care costs under various disease progression scenarios to compare the costs and benefits of antiretroviral therapy. RESULTS The analysis suggests that: (1) recent projections of long-term medical care cost savings due to highly effective protease inhibitor combination therapies are probably illusory; (2) it makes relatively little difference to the overall long-term cost of HIV/AIDS care whether combination antiretroviral therapy completely prevents or just substantially delays progression to AIDS; and (3) although combination therapy is not likely to save economic resources in the long run, it nevertheless can be highly cost effective. CONCLUSIONS The health-related benefits of antiretroviral therapy are not free, but appear to be worth the cost.
Class I That Recognizes the C1 Epitope of MHC Lacking an Activating NK Cell Receptor Humans Differ from Other Hominids in

Modulation of human NK cell function by killer cell Ig-like receptors (KIR) and MHC class I is dominated by the bipartite interactions of inhibitory lineage III KIR with the C1 and C2 epitopes of HLA-C. In comparison, the ligand speciﬁcities and functional contributions of the activating lineage III KIR remain poorly understood. Using a robust, sensitive assay of KIR binding and a representative panel of 95 HLA class I targets, we show that KIR2DS1 binds C2 with ∼ 50% the avidity of KIR2DL1, whereas KIR2DS2, KIR2DS3, and KIR2DS5 have no detectable avidity for C1, C2, or any other HLA class I epitope. In contrast, the chimpanzee has activating C1- and C2-speciﬁc lineage III KIR with strong avidity, comparable to those of their paired inhibitory receptors. One variant of chimpanzee Pt–KIR3DS2, the activating C2-speciﬁc receptor, has the same avidity for C2 as does inhibitory Pt–KIR3DL4, and a second variant has ∼ 73% the avidity. Chimpanzee Pt– KIR3DS6, the activating C1-speciﬁc receptor, has avidity for C1 that is ∼ 70% that of inhibitory Pt–KIR2DL6. In both humans and chimpanzees we observe an evolutionary trend toward reducing the avidity of the activating C1- and C2-speciﬁc receptors through selective acquisition of attenuating substitutions. However, the extent of attenuation has been extreme in humans, as exempliﬁed by KIR2DS2, an activating C1-speciﬁc receptor that has lost all detectable avidity for HLA class I. Supporting such elimination of activating C1-speciﬁc receptors as a related inhibitory
Level of vascular endothelial growth factor in tenon tissue and results of glaucoma surgery.

OBJECTIVE To determine the levels of vascular endothelial growth factor (VEGF) in both the aqueous humor and Tenon tissue in patients with primary open angle glaucoma (POAG) and the associations between the VEGF and outcomes of glaucoma surgery. METHODS The study involved 19 patients with POAG who were scheduled to undergo glaucoma surgery owing to uncontrolled intraocular pressure (IOP) and 17 control subjects who were scheduled to undergo cataract surgery. At the time of surgery, about 0.1 mL of aqueous humor was collected through an anterior chamber paracentesis and a 44-mm Tenon tissue sample was cut from the eye. Concentrations of VEGF were analyzed by enzyme-linked immunosorbent assay. Spearman correlation and regression analysis were used to assess the relationship with VEGF level to the clinical characteristics and postoperative IOP. RESULTS The VEGF in Tenon tissue was significantly elevated in patients with POAG compared with control subjects(P=.001). When patients with POAG were divided into success or failure groups 1 year following surgery, the VEGF levels were significantly higher in the Tenon tissue of the failure group compared with the success group(P=.014). The preoperative IOP was significantly related to the VEGF level in Tenon tissue in both the univariate(P=.001) and multivariate (P=.012) regressions. CONCLUSIONS The VEGF level in Tenon tissue at the time of surgery was significantly related to 1-year surgical outcomes of glaucoma surgery, and it was significantly associated with the final IOP in patients with POAG.
The human growth hormone gene is regulated by a multicomponent locus control region

The five-member human growth hormone (hGH)/chorionic somatomammotropin (hCS) gene cluster encodes the pituitary-specific hGH-N gene and four highly related genes (hGH-V, hCS-A, hCS-B, and hCS-L) that are expressed only in the placenta. When the hGH-N or hCS-A gene, together with all previously identified cis-acting regulatory sequences, was integrated into the mouse genome, it was expressed only sporadically and at low levels in the transgenic target organs. DNase I mapping of chromatin from expressing and nonexpressing cell types was used to identify a pituitary-specific set of DNase I-hypersensitive sites (HS) and a set of HS common to both the pituitary and placenta, centered approximately 15 and 30 kb 5' of hGH-N, respectively. When contained on a cosmid insert in their native genomic configuration, these HS consistently directed high-level, pituitary-specific expression of hGH-N in transgenic mice and appeared to define a locus control region required for hGH-N expression. Individually, each set of HS was able to mediate position-independent hGH-N expression in the pituitary but demonstrated loss of physiologic control and loss of tissue specificity. The gene-proximal set of HS contained a potent enhancer activity in the pituitary, while the more distal set appeared to function primarily to establish site-of-integration independence. These data indicate that synergistic interactions among multiple elements are required to restrict hGH-N transcription to the pituitary and generate appropriate levels of expression. In addition, these results suggest a role for both shared and unique regulatory sequences in locus control region-mediated expression of the hGH/hCS gene cluster in the pituitary and possibly the placenta.
High frequency synchrony in the cerebellar cortex during goal directed movements

The cerebellum is involved in sensory-motor integration and cognitive functions. The origin and function of the field potential oscillations in the cerebellum, especially in the high frequencies, have not been explored sufficiently. The primary objective of this study was to investigate the spatio-temporal characteristics of high frequency field potentials (150–350 Hz) in the cerebellar cortex in a behavioral context. To this end, we recorded from the paramedian lobule in rats using micro electro-corticogram (μ-ECoG) electrode arrays while the animal performed a lever press task using the forelimb. The phase synchrony analysis shows that the high frequency oscillations recorded at multiple points across the paramedian cortex episodically synchronize immediately before and desynchronize during the lever press. The electrode contacts were grouped according to their temporal course of phase synchrony around the time of lever press. Contact groups presented patches with slightly stronger synchrony values in the medio-lateral direction, and did not appear to form parasagittal zones. The size and location of these patches on the cortical surface are in agreement with the sensory evoked granular layer patches originally reported by Welker's lab (Shambes et al., 1978). Spatiotemporal synchrony of high frequency field potentials has not been reported at such large-scales previously in the cerebellar cortex.
Quadrocopter ball juggling

This paper presents a method allowing a quadrocopter with a rigidly attached racket to hit a ball towards a target. An algorithm is developed to generate an open loop trajectory guiding the vehicle to a predicted impact point - the prediction is done by integrating forward the current position and velocity estimates from a Kalman filter. By examining the ball and vehicle trajectories before and after impact, the system estimates the ball's drag coefficient, the racket's coefficient of restitution and an aiming bias. These estimates are then fed back into the system's aiming algorithm to improve future performance. The algorithms are implemented for three different experiments: a single quadrocopter returning balls thrown by a human; two quadrocopters co-operatively juggling a ball back-and-forth; and a single quadrocopter attempting to juggle a ball on its own. Performance is demonstrated in the Flying Machine Arena at the ETH Zurich.
Polarimetric Contextual Classification of PolSAR Images Using Sparse Representation and Superpixels

In recent years, sparse representation-based techniques have shown great potential for pattern recognition problems. In this paper, the problem of polarimetric synthetic aperture radar (PolSAR) image classification is investigated using sparse representation-based classifiers (SRCs). We propose to take advantage of both polarimetric information and contextual information by combining sparsity-based classification methods with the concept of superpixels. Based on polarimetric feature vectors constructed by stacking a variety of polarimetric signatures and a superpixel map, two strategies are considered to perform polarimetric-contextual classification of PolSAR images. The first strategy starts by classifying the PolSAR image with pixel-wise SRC. Then, spatial regularization is imposed on the pixel-wise classification map by using majority voting within superpixels. In the second strategy, the PolSAR image is classified by taking superpixels as processing elements. The joint sparse representation-based classifier (JSRC) is employed to combine the polarimetric information contained in feature vectors and the contextual information provided by superpixels. Experimental results on real PolSAR datasets demonstrate the feasibility of the proposed approaches. It is proven that the classification performance is improved by using contextual information. A comparison with several other approaches also verifies the effectiveness of the proposed approach.
The all-or-nothing multicommodity flow problem

We consider the all-or-nothing multicommodity flow problem in general graphs. We are given a capacitated undirected graph <i>G</i>=(<i>V,E,u</i>) and set of <i>k</i> pairs <i>s</i><inf>1</inf> <i>t</i><inf>1</inf>, <i>s</i><inf>2</inf><i>t</i><inf>2</inf>, …, <i>s<inf>k</inf>t<inf>k</inf></i>. Each pair has a unit demand. The objective is to find a largest subset <i>S</i> of 1,2,…,<i>k</i> such that for every <i>i</i> in <i>S</i> we can send a flow of one unit between <i>s<inf>i</inf></i> and <i>t<inf>i</inf></i>. Note that this differs from the <i>edge-disjoint path</i> problem (<sc>EDP</sc>) in that we do not insist on integral flows for the pairs. This problem is NP-hard, and APX-hard, even on trees. For trees, a 2--approximation is known for the cardinality case and a 4--approximation for the weighted case. In this paper we build on a recent result of Räcke on low congestion oblivious routing in undirected graphs to obtain a poly-logarithmic approximation for the all-or-nothing problem in <i>general</i> undirected graphs. The best previous known approximation for all-or-nothing flow problem was <i>O</i>(min(<i>n</i><<sup>2/3</sup>, √<i>m</i>)), the same as that for <sc>EDP</sc>. Our algorithm extends to the case where each pair <i>s<inf>i</inf>t<inf>i</inf></i> has a demand <i>d<sup>i</sup></i> associated with it and we need to completely route <i>d<sup>i</sup></i> to get credit for pair <i>i</i>. We also consider the <i>online admission control</i> version where pairs arrive online and the algorithm has to decide immediately on its arrival whether to accept it or not. We obtain a randomized algorithm with a competitive ratio that is similar to the approximation ratio for the offline algorithm.
Revisiting the Basic Reproductive Number for Malaria and Its Implications for Malaria Control

The prospects for the success of malaria control depend, in part, on the basic reproductive number for malaria, R 0. Here, we estimate R 0 in a novel way for 121 African populations, and thereby increase the number of R 0 estimates for malaria by an order of magnitude. The estimates range from around one to more than 3,000. We also consider malaria transmission and control in finite human populations, of size H. We show that classic formulas approximate the expected number of mosquitoes that could trace infection back to one mosquito after one parasite generation, Z 0(H), but they overestimate the expected number of infected humans per infected human, R 0(H). Heterogeneous biting increases R 0 and, as we show, Z 0(H), but we also show that it sometimes reduces R 0(H); those who are bitten most both infect many vectors and absorb infectious bites. The large range of R 0 estimates strongly supports the long-held notion that malaria control presents variable challenges across its transmission spectrum. In populations where R 0 is highest, malaria control will require multiple, integrated methods that target those who are bitten most. Therefore, strategic planning for malaria control should consider R 0, the spatial scale of transmission, human population density, and heterogeneous biting.
Retrospective: virtual memory mapped network interface for the SHRIMP multicomputer

This paper is the first paper reporting the SHRIMP project at Princeton [l]. It describes the design of a network interface that implements a virtual memory-mapped communication model for protected, user-level communication. The vision of the SHRIMP project was to investigate how to use commodity PCs and commodity software (including operating systems) as building blocks to construct scalable, inexpensive servers that can deliver performance comparable to or better than custom-designed multicomputers. A challenge was to deliver communication performance to applications that was close to the hardware limit. This paper was the result of our effort to design network interfaces to support protected, user-level communication. In this retrospective, we would like to describe where our ideas came from, how the research project started, how we wrote the paper, how well the ideas worked out, and the current state of the SHRIMP project.
JavaBST: Java backward slicing tool

Program slicing is a technique of abstracting from a program depending on slicing criteria to be used in maintenance, debugging and other applications. Java programs as any other programming language has been a target for slicing tool, such as Kaveri and WALA. In this paper, we present a new Java backward slicing tool; JavaBST. JavaBST, proposed a new way of reading java code and produce the dependencies depending on the syntax to produce a backward slice for each variable in the program. It succeeded in terms of producing slices. But, still simple tool to deal with complicated programs.
The role of synovial macrophages and macrophage-produced mediators in driving inflammatory and destructive responses in osteoarthritis.

Osteoarthritis (OA), one of the most common diseases among humans, is characterised pathologically by focal areas of damage on articular cartilage centred on load-bearing areas, associated with formation of new bone at the joint margins and changes in subchondral bone. Given the huge economic and personal burden of OA, and the fact that this disease is the major cause for the increasing demand for joint replacements, there is urgent need for disease modifying treatments to stop or at least slow the development and progression of OA. But for this to be possible, we need further knowledge about the pathogenesis of disease initiation and progression in OA. The great success of targeted biologic therapy against rheumatoid arthritis (RA) in recent years has meant that much research has been devoted to investigating the pathophysiology of osteoarthritis (OA), in the hope of defining novel therapeutic targets. In contrast to RA, with its pannus and erosions, OA has long been thought of as a degenerative disease of cartilage, with secondary bony damage and osteophytes. In recent years, the importance of the synovium, and in particular the synovial macrophages, in OA, has been highlighted in both in vitro and in vivo studies. This article will give an overview of some important recent findings concerning the ability of macrophages to drive inflammatory and destructive disease mechanisms in OA, the role of their proinflammatory cytokines in doing so, and the potential for macrophages and macrophage-produced cytokines to be used as therapeutic targets for the development of disease-modifying anti-ostroarthritic drugs (DMOADs). There is also an abundance of potential downstream therapeutic targets in OA, including the matrix metalloproteinases, the aggrecanases, the inducible nitric oxide synthetase, and elements of the Wnt pathway.
Mining Surprising Patterns Using Temporal Description Length

We propose a new notion of surprising temporal patterns in market basket data, and algorithms to (cid:12)nd such patterns. This is distinct from (cid:12)nding frequent patterns as addressed in the common mining literature. We argue that once the analyst is already familiar with prevalent patterns in the data, the greatest incremental bene(cid:12)t is likely to be from changes in the relationship between item frequencies over time. A simple measure of surprise is the extent of departure from a model, estimated using standard multivariate time series analysis. Unfortunately, such estimation involves models, smoothing windows and parameters whose optimal choices can vary dramatically from one application to another. In contrast, we propose a precise characterization of surprise based on the number of bits in which a basket sequence can be encoded under a carefully chosen coding scheme. In this scheme it is inexpensive to encode sequences of itemsets that have steady, hence likely to be well-known, correlation between items. Conversely, a sequence with large code length hints at a possibly surprising correlation. Our notion of surprise also has the desirable property that the score of a set of items is o(cid:11)set by anything surprising that the user may already know from the marginal distribution of any proper subset. No parameters, such as support, con(cid:12)dence, or smoothing windows, need to be estimated or speci(cid:12)ed by the user. We experimented with real-life market basket data. The algorithm successfully rejected a large number of frequent sets of items that bore obvious and steady complementary relations to each other, such as cereal and milk. Instead, our algorithm found itemsets that showed statistically strong (cid:13)uctuations in correlation over time. These items had no obviously complementary roles.
Vision-based motion control for a hitting task-Hanetsuki

We describe our approach to the robotic Hanetsuki task (Japanese badminton), that is, to return the incoming shuttlecock to the human's side with a racket. A learning method using a novel database is proposed to compensate for the insufficiency in a model-based approach. Experimental results obtained with the developed Hanetsuki robot are presented. <<ETX>>