Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Genome Analysis Provides Insights into the Evolution and Adaptation of Pseudomonas syringae pv. aesculi on Aesculus hippocastanum

A recently emerging bleeding canker disease, caused by Pseudomonas syringae pathovar aesculi (Pae), is threatening European horse chestnut in northwest Europe. Very little is known about the origin and biology of this new disease. We used the nucleotide sequences of seven commonly used marker genes to investigate the phylogeny of three strains isolated recently from bleeding stem cankers on European horse chestnut in Britain (E-Pae). On the basis of these sequences alone, the E-Pae strains were identical to the Pae type-strain (I-Pae), isolated from leaf spots on Indian horse chestnut in India in 1969. The phylogenetic analyses also showed that Pae belongs to a distinct clade of P. syringae pathovars adapted to woody hosts. We generated genome-wide Illumina sequence data from the three E-Pae strains and one strain of I-Pae. Comparative genomic analyses revealed pathovar-specific genomic regions in Pae potentially implicated in virulence on a tree host, including genes for the catabolism of plant-derived aromatic compounds and enterobactin synthesis. Several gene clusters displayed intra-pathovar variation, including those encoding type IV secretion, a novel fatty acid biosynthesis pathway and a sucrose uptake pathway. Rates of single nucleotide polymorphisms in the four Pae genomes indicate that the three E-Pae strains diverged from each other much more recently than they diverged from I-Pae. The very low genetic diversity among the three geographically distinct E-Pae strains suggests that they originate from a single, recent introduction into Britain, thus highlighting the serious environmental risks posed by the spread of an exotic plant pathogenic bacterium to a new geographic location. The genomic regions in Pae that are absent from other P. syringae pathovars that infect herbaceous hosts may represent candidate genetic adaptations to infection of the woody parts of the tree.
Maternal histone variants and their chaperones promote paternal genome activation and boost somatic cell reprogramming

The mammalian egg employs a wide spectrum of epigenome modification machinery to reprogram the sperm nucleus shortly after fertilization. This event is required for transcriptional activation of the paternal/zygotic genome and progression through cleavage divisions. Reprogramming of paternal nuclei requires replacement of sperm protamines with canonical and non‐canonical histones, covalent modification of histone tails, and chemical modification of DNA (notably oxidative demethylation of methylated cytosines). In this essay we highlight the role maternal histone variants play during developmental reprogramming following fertilization. We discuss how reduced maternal histone variant incorporation in somatic nuclear transfer experiments may explain the reduced viability of resulting embryos and how knowledge of repressive and activating maternal factors may be used to improve somatic cell reprogramming.
Social Network Applications using Cellular Phones with E-mail Function

Recently, there has been an increasing interest in social networking, in which users can form new relationships between friends by introducing friends with each other. In this paper, we describe the design and implementation of a query propagation mechanism and its applications to realize a social network composed of mobile users. Our realized social network consists of multiple mobile phones and a server with the query propagation mechanism.
Neurophysiological Indexes of Speech Processing Deficits in Children with Specific Language Impairment

We used neurophysiological and behavioral measures to examine whether children with specific language impairment (SLI) have deficits in automatic processing of brief, phonetically similar vowels, and whether attention plays a role in such deficits. The neurophysiological measure mismatch negativity (MMN) was used as an index of discrimination in two tasks; one in which children ignored the auditory stimuli and watched a silent video and a second in which they attended to the auditory modality. Children with SLI showed good behavioral discrimination, but significantly poorer behavioral identification of the brief vowels than the children with typical language development (TLD). For the TLD children, two neurophysiological measures (MMN and a later negativity, LN) indexed discrimination of the vowels in both tasks. In contrast, only the LN was elicited in either task for the SLI group. We did not see a direct correspondence between the absence of MMN and poor behavioral performance in the children with SLI. This pattern of findings indicates that children with SLI have speech perception deficiencies, although the underlying cause may vary.
Periovulatory changes in hypothalamic and pituitary monoamines following GnRH analogue treatment in the catfish Heteropneustes fossilis: a study correlating changes in plasma hormone profiles.

In Heteropneustes fossilis, administration of a single dose (0.15 micrograms/g body weight, i.p.) of [D-Ala6,Gly10]-gonadotrophin-releasing hormone analogue (GnRHa) induced ovulation (in 35 of 35 fish) when mild-stripped at 16 h. Plasma gonadotrophin II (GTH II) levels showed a highly significant increase at 2, 4, 8, 12 and 16 h with the peak at 8 h. Plasma cortisol, progesterone and testosterone showed significant elevations at 2, 4, 8 and 12 h with peaks at 8 h (cortisol and testosterone) and 4 h (progesterone). The levels declined to control values at 16 and 48 h except that of testosterone which decreased even further. In contrast, plasma levels of oestradiol-17 beta decreased significantly at 2, 4, 8 and 12 h, with the lowest value at 8 h, but increased at 16 and 18 h. The contents of hypothalamic and pituitary serotonin and noradrenaline increased at 8 h, coinciding with the peak GTH II rise, and decreased at 16 h. In contrast, dopamine content declined at 8 h in both the hypothalamus and pituitary, but increased at 16 h only in the hypothalamus. The hypothalamic adrenaline level decreased at 8 h but increased significantly at 16 h. Hypothalamic levels of monoamine oxidase, catechol O-methyltransferase and dopamine beta-hydroxylase were elevated significantly at 8 h; the dopamine beta-hydroxylase activity decreased at 16 h. Phenylethanolamine N-methyltransferase activity was elevated only at 16 h, coinciding with the rise in adrenaline content. It is inferred that the preovulatory decrease in dopamine content concomitant with rises in serotonin and noradrenaline levels, triggered by the low titre of oestradiol, might have potentiated the GnRHa/GnRH (endogenous)-induced release of GTH II for a prolonged period.
Instrumental role of Na+ in NMDA excitotoxicity in glucose‐deprived and depolarized cerebellar granule cells

In glucose‐deprived cerebellar granule cells, substitution of extracellular Na+ with Li+ or Cs+ prevented N‐methyl‐d‐aspartate (NMDA)‐induced excitotoxicity. NMDA stimulated 45Ca2+ accumulation and ATP depletion in a Na‐dependent manner, and caused neuronal death, even if applied while Na,K‐ATPase was inhibited by 1 mm ouabain. The cells treated with NMDA in the presence of ouabain accumulated sizable 45Ca2+ load but most of them failed to elevate cytosolic [Ca2+] upon mitochondrial depolarization. Na/Ca exchange inhibitor, KB‐R7943, inhibited Na‐dependent and NMDA‐induced 45Ca2+ accumulation but only if Na,K‐ATPase activity was compromised by ouabain. In cells energized by glucose and exposed to NMDA without ouabain, KB‐R7943 reduced NMDA‐elicited ionic currents by 19% but failed to inhibit 45Ca2+ accumulation. It appears that a large part of NMDA‐induced Ca2+ influx in depolarized and glucose‐deprived cells is mediated by reverse Na/Ca exchange. A high level of reverse Na/Ca exchange operation is maintained by a sustained Na+ influx via NMDA channels and depolarization of the plasma membrane. In cells energized by glucose, however, most Ca2+ enters directly via NMDA channels because Na,K‐ATPase regenerating Na+ and K+ concentration gradients prevents Na/Ca exchange reversal. Since under these conditions Na/Ca exchange extrudes Ca2+, its inhibition destabilizes Ca2+ homeostasis.
Applying Contextual Design to Build a Course Scheduler: A Case Study

This paper describes the design of a course-scheduling tool that assists professors in planning events such as tests, assignments and lectures. It takes university calendar information along with user inputs of course events, and translates these into algebraic constraints, which are then solved by a linear programming algorithm to generate a feasible schedule. We report on the application of the Contextual Design [1] methodology to generate requirements and architecture of this tool. First, a contextual analysis was conducted to ensure that specifications were adequately developed. This included conducting and coding interviews with potential users, and gathering and analyzing work artifacts. Then a prototype was implemented and evaluated by means of a cognitive walkthrough. By describing the design process and the resulting system, this paper makes two contributions. First, it illustrates the contextual approach to interactive system design in an educational domain. Second, it presents the architecture of a course-scheduling tool, with a constraint-solver based on the linear programming algorithm at its heart, which allows the automatic creation of feasible event schedules.
Fathers' experiences during pregnancy: Paternal prenatal attachment and representations of the fetus

Positive attachment experiences during infancy are linked to positive developmental outcomes of children later in life. The parent–infant relationship does not start upon the birth of the child, but already evolves during pregnancy. In this exploratory study, fathers’ experiences during pregnancy are investigated, focusing on their relationship with the unborn baby. At 26 weeks gestational age, expectant fathers from a Dutch community-based sample (N = 301) completed questionnaires concerning feelings of attachment to the fetus and psychological well-being. The semistructured Working Model of the Child Interview was conducted to assess the “meaning” the unborn child has to the father (i.e., the internal representation of the fetus). Results show that the quality of fathers’ prenatal attachment and their representations of the fetus were interrelated. Fathers who reported a higher quality of prenatal attachment were more likely to have balanced representations of their unborn children, whereas fathers with a lower quality of attachment were more likely to show disengaged representations. Furthermore, the quality of fathers’ self-reported prenatal attachment was higher when fathers experienced fewer symptoms of depression and anxiety during pregnancy, when they were younger, and when they expected their first child. These factors were not significantly related to fathers’ internal representations of the fetus. Further research is needed to examine the effects of the prenatal father–infant relationship on postnatal father–child attachment, infant behavior, and infant development.
Radioprotective effect of American ginseng on human lymphocytes at 90 minutes postirradiation: a study of 40 cases.

BACKGROUND Ionizing radiation (IR) initiates intracellular oxidative stress through enhanced formation of reactive oxygen species (ROS) that attack DNA leading to cell death. Because of the diversity of IR applied in medicine, agriculture, industry, and the growing threats of global terrorism, the acquisition of radioprotectors is an urgent need for the nation. However, the applicability of radioprotectors currently under investigation is limited due to their inherent toxicity. OBJECTIVE This study investigated the effect of a standardized North American ginseng extract (NAGE, total ginsenoside content: 11.7%) on DNA damage in human lymphocytes at 90 minutes postirradiation. DESIGN With the application of NAGE (250-1000 microg mL(-1)) at 90 minutes postirradiation (1 and 2 Gy), DNA damage in lymphocytes obtained from 40 healthy individuals was evaluated by cytokinesis-block micronucleus assay. Similar experiments were also performed in lymphocytes treated with WR-1065 (1 mmol/L or 3 mmol/L). In addition, before and after irradiation, lymphocytes obtained from 10 individuals were measured for their total antioxidant capacity (TAC) and the reactive oxygen species (ROS). RESULTS The significant effect of NAGE against (137)Cs-induced micronuclei (MN) in lymphocytes is concentration dependent. NAGE (750 microg mL(-1)) reduced MN yield by 50.7% after 1 Gy and 35.9% after 2 Gy exposures, respectively; these results were comparable to that of WR-1065. Furthermore, we also found that NAGE reduces MN yield and ROS but increases TAC in lymphocytes. CONCLUSIONS Our results suggest that NAGE is a relatively nontoxic natural compound that holds radioprotective potential in human lymphocytes even when applied at 90 minutes postirradiation. One of the radioprotective mechanisms may be mediated through the scavenging of free radicals and enhancement of the intracellular TAC.
Depletion of B lymphocytes in chronic hypoplastic marrow failure (aplastic anaemia).

Summary: The numbers of B and T lymphocytes were measured in nine patients with chronic hypoplastic mar-row failure and significant depletion of B but not of T lymphocytes was found. The lesion in the disease therefore appears to affect lymphopoiesis in addition to myelopoiesis. Study of surface immunoglobulin markers in three patients provided no evidence of clonal nature of the lymphocytes in the disease.
Highlighting Psychological Features for Predicting Child Interjections During Story Telling

Conversational agents are more and more investigated by the community but their ability to keep the user committed in the interaction is limited. Predicting the behavior of children in a human-machine interaction setting is a key issue for the success of narrative conversational agents. In this paper, we investigate solutions to evaluate the child’s commitment in the story and to detect when the child is likely to react during the story. We show that the conversational agent cannot solely count on questions and requests for attention to stimulate the child. We assess how (1) psychological features allow to improve the prediction of children interjections and how (2) exploiting these features with Pattern Mining techniques offers better results. Experiments show that psychological features improves the predictions and furthermore help to produce robust dialog models.
Preferential assembly of heteromeric small conductance calcium‐activated potassium channels

The activation of small conductance calcium‐dependent (SK) channels regulates membrane excitability by causing membrane hyperpolarization. Three subtypes (SK1‐3) have been cloned, with each subtype expressed within the nervous system. The locations of channel subunits overlap, with SK1 and SK2 subunits often expressed in the same brain region. We showed that expressed homomeric rat SK1 subunits did not form functional channels, because subunits accumulated in the Golgi. This raised the question of whether heteromeric channels could form with SK1 subunits. The co‐expression of SK1 and SK2 subunits in HEK293 cells preferentially co‐assembled to produce heteromeric channels with a fixed stoichiometry of alternating subunits. The expression in hippocampal CA1 neurons of mutant rat SK1 subunits [rat SK1(LV213/4YA)] that produced an apamin‐sensitive current changed the amplitude and pharmacology of the medium afterhyperpolarization. The overexpression of rat SK1(LV213/4YA) subunits reduced the sensitivity of the medium afterhyperpolarization to apamin, substantiating the preferential co‐assembly of SK1 and SK2 subunits to form heteromeric channels. Species‐specific channel assembly occurred as the co‐expression of human SK1 with rat SK2 did not form functional heteromeric channels. The replacement of two amino acids within the C‐terminus of rat SK2 with those from human SK2 permitted the assembly of heteromeric channels when co‐expressed with human SK1. These data showed that species‐specific co‐assembly was mediated by interaction between the C‐termini of SK channel subunits. The finding that SK channels preferentially co‐assembled to form heteromeric channels suggested that native heteromeric channels will predominate in cells expressing multiple SK channel subunits.
An efficient algorithm for 3D reluctance extraction considering high frequency effect

As shown in literatures, partial reluctance based circuit analysis is efficient in capturing on-chip inductance effect, because the partial reluctance exhibits much better locality than partial inductance. However, most previous works on reluctance extraction did not take high frequency effect into account and were not efficient enough for 3D complex structure. In this paper, a new reluctance extraction algorithm is proposed considering the high frequency effect. Numerical experiments demonstrate that our algorithm can handle complex 3D interconnect structures while exhibiting high accuracy and a speed-up ratio of several tens to hundreds over FastHenry
THE EARLY POSTTRANSPLANT PROGNOSIS OF ACUTE RENAL ALLOGRAFT REJECTION AS DETERMINED BY DETECTION OF CYTOTOXIC ANTIBODIES TO LYMPHOID B CELL LINES

We have studied serial samples of pretransplant and posttransplant sera for cytotoxic antibodies to lymphoid B cell lines (LCL) in 45 renal allograft recipients. A total of 48 rejection reactions occurred in 31 patients. A comparison of each patient's most reactive posttransplant serum showed a significantly higher reactivity in the ten patients with early allograft failure when compared with the 21 patients with reversible rejections and the 14 patients who had no rejections. Rejection reactions were easily differentiated by comparing the change in cytotoxic reactivity to LCL of recipients' sera drawn at the time of a rejection episode with the reactivity of their pretransplant sera. In 32 rejections considered non-antibody-associated cytotoxic reactivity of recipients' sera to LCL either decreased or remained essentially unchanged during the rejection. In 16 rejections considered antibody-associated the recipients' sera drawn during the rejection episode showed an increase in cytotoxic reactivity ranging from 40% to 100%. Response to antirejection therapy and three month graft survival had a significant correlation with changes in LCL antibody reactivity during a rejection. Only two of the 32 rejections considered non-antibody-associated failed to reverse compared with eight of the 16 antibody-associated rejections (P<.001). Graft survival at three months in patients with non-antibody-associated rejections was 90% compared with 27% in the 11 patients who had antibody-associated rejections (P <.001). Other parameters possibly related to the severity of a rejection reaction or to early allograft prognosis did not differ appreciably between the two types of rejections. This included the time posttransplant to the first rejection episode, the number of patients with multiple rejections in the first three months, and rejections requiring dialysis therapy. Determination of a change in cytotoxic reactivity to LCL during a rejection reaction enables one to predict the response to antirejection therapy and early allograft prognosis. This may ultimately be useful in selecting different types of antirejection therapy for individual patients.
Computing energy-efficiency in the mobile GPU

In this paper, we explain the energy-efficiency of mobile GPU through the performance and power comparisons of CPU and GPU integrated in the ARM processor-based System-on-Chip. Two kinds of application processors (GPGPU with 72.5GFLOPS computing capability integrated with 1.7GHz dual-core ARMv7A architecture CPUs and GPGPU with 108.7GFLOPS computing capability integrated with 1.8/1.3GHz octa-core ARMv7A architecture CPUs) are used in the experiment. The power and performance analyses of Kishonti Informatics' CLBenchmark and embedded image processing test suite of Renderscript can provide that the GPU based general-purpose computing ability can deliver 10x higher energy-efficiency in compute-intensive multimedia applications, compared with a CPU solution [1]. The GPU benefits arise from its parallel architecture, which is well suited for compute-intensive multimedia applications. Consequently, a high-performance GPU delivers higher energy-efficiency than any combination of CPU and GPU in most case of compute-intensive workloads.
Corpus-Induced Corpus Clean-up

We explore the feasibility of using only unsupervised means to identify non-words, i.e. typos, in a frequency list derived from a large corpus of Dutch and to distinguish between these non-words and real-words in the language. We call the system we built and evaluate in this paper ciccl, which stands for Corpus-Induced Corpus Clean-up. The algorithm on which ciccl is primarily based is the anagram-key hashing algorithm introduced by (Reynaert, 2004). The core correction mechanism is a simple and effective method which translates the actual characters which make up a word into a large natural number in such a way that all the anagrams, i.e. all the words composed of precisely the same subset of characters, are allocated the same natural number. In effect, this constitutes a novel approximate string matching algorithm for indexed text search. This is because by simple addition, subtraction or a combination of both, all variants within reach of the range of numerical values defined in the alphabet are retrieved by iterating over the alphabet. ciccl's input consists primarily of corpus derived frequency lists, from which it derives valuable morphological information by performing frequency counts over the substrings of the words, which are then used to perform decompounding, as well as for distinguishing between most likely correctly spelled words and typos.
Radiolysis of nucleosides in aqueous solutions: base liberation by the base attack mechanism.

On the radiolysis of uridine and some other nucleosides in aqueous solution, a pH-dependent liberation of uracil or the corresponding base was found. e-aq and HO-. 2 gave no freed bases, although many oxidizing radicals, including OH, Cl-. 2, Br-. 2, (CNS)-. 2 and SO-. 4, did cause the release of unaltered bases, depending on the pH of the solutions. The base yields were generally high at pH greater than or equal to 11, with the exception of SO-. 4, which gave a rather high yield of uracil (from uridine) even in the pH region of less than or equal to 11. The pattern of the base formation against pH varied with the reacting radical, but was the same for the different nucleosides. With regard to the OH radical system, bases are considered to be formed after H-abstraction of the sugar moiety at low pH. The other oxidizing radicals, however, may cause base release by attack at the base. It is possible that O-, present at high pH as the dissociated form of OH, may act partly as an oxidizing radical. A plausible mechanism of 31'-radical formation is discussed.
A comparison of neural network and Bayes recognition approaches to the diagnostic of multiple sclerosis

This article describes the application of a Multi-Layer Perceptron (MLP) to the problem of diagnosing Multiple Sclerosis (MS). The classification information is obtained by a Trigeminal Evoked Potential (TEP) test. The performance of the MLP is compared with that of the human experts and the Bayes classifier. The efficiency of the neural network and the classical classifiers in conjunction with 4 types of features - the Fourier transform (FT), the peak position, the ARX model coefficient and the temporal wave form - are examined. Although a large clinical data base would be necessary, before this approach can be fully validated, the initial results are very promising. The MLP was found to be less susceptible to the number of features used. The ability of the MLP classifier to generalize is far better than that of the Bayes classifier.