Miracle-dz/UniFAR-FTUs huggingface dataset:
Analyzing the Effects of Human-Aware Motion Planning on Close-Proximity Human–Robot Collaboration

Objective: The objective of this work was to examine human response to motion-level robot adaptation to determine its effect on team fluency, human satisfaction, and perceived safety and comfort. Background: The evaluation of human response to adaptive robotic assistants has been limited, particularly in the realm of motion-level adaptation. The lack of true human-in-the-loop evaluation has made it impossible to determine whether such adaptation would lead to efficient and satisfying human–robot interaction. Method: We conducted an experiment in which participants worked with a robot to perform a collaborative task. Participants worked with an adaptive robot incorporating human-aware motion planning and with a baseline robot using shortest-path motions. Team fluency was evaluated through a set of quantitative metrics, and human satisfaction and perceived safety and comfort were evaluated through questionnaires. Results: When working with the adaptive robot, participants completed the task 5.57% faster, with 19.9% more concurrent motion, 2.96% less human idle time, 17.3% less robot idle time, and a 15.1% greater separation distance. Questionnaire responses indicated that participants felt safer and more comfortable when working with an adaptive robot and were more satisfied with it as a teammate than with the standard robot. Conclusion: People respond well to motion-level robot adaptation, and significant benefits can be achieved from its use in terms of both human–robot team fluency and human worker satisfaction. Application: Our conclusion supports the development of technologies that could be used to implement human-aware motion planning in collaborative robots and the use of this technique for close-proximity human–robot collaboration.
Efficient Production of l-Ribose with a Recombinant Escherichia coli Biocatalyst

ABSTRACT A new synthetic platform with potential for the production of several rare sugars, with l-ribose as the model target, is described. The gene encoding the unique NAD-dependent mannitol-1-dehydrogenase (MDH) from Apium graveolens (garden celery) was synthetically constructed for optimal expression in Escherichia coli. This MDH enzyme catalyzes the interconversion of several polyols and their l-sugar counterparts, including the conversion of ribitol to l-ribose. Expression of recombinant MDH in the active form was successfully achieved, and one-step purification was demonstrated. Using the created recombinant E. coli strain as a whole-cell catalyst, the synthetic utility was demonstrated for production of l-ribose, and the system was improved using shaken flask experiments. It was determined that addition of 50 to 500 μM ZnCl2 and addition of 5 g/liter glycerol both improved production. The final levels of conversion achieved were >70% at a concentration of 40 g/liter and >50% at a concentration of 100 g/liter. The best conditions determined were then scaled up to a 1-liter fermentation that resulted in 55% conversion of 100 g/liter ribitol in 72 h, for a volumetric productivity of 17.4 g liter−1 day−1. This system represents a significantly improved method for the large-scale production of l-ribose.
Comparative genomics of the lactic acid bacteria

Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.
Spinal Neuronal NOS Signaling Contributes to Morphine Cardioprotection in Ischemia Reperfusion Injury in Rats

Morphine has been widely used as rescue treatment for heart attack and failure in humans for many decades. Relatively little has been known about the role of spinal opioid receptors in morphine cardioprotection. Recent studies have shown that intrathecal injection of morphine can reduce the heart injury caused by ischemia (I)/reperfusion (R) in rats. However, the molecular and cellular mechanisms underlying intrathecal morphine cardioprotection has not been determined. Here, we report that intrathecal morphine postconditioning (IMPOC) rescued mean artery pressure (MAP) and reduced myocardial injury in I/R. Pretreatment with either naloxone (NAL), a selective mu-opioid receptor antagonist, or nitric oxide synthase (NOS) inhibitors via intrathecal delivery completely abolished IMPOC cardioprotection, suggesting that the spinal mu-opioid receptor and its downstream NOS signaling pathway are involved in the mechanism of the morphine-induced effect. Consistent with this, IMPOC significantly enhanced spinal neural NOS phosphorylation, nitric oxide, and cGMP content in a similar time course. Intrathecal application of 1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one, a specific inhibitor of guanylate cyclase, completely ablated IMPOC-induced enhancement of cardioprotection and spinal cGMP content. IMPOC rescue of MAP and ischemic injury is correlated with IMPOC enhancement of NOS signaling. Collectively, these findings strengthen the concept of spinal mu-opioid receptors as a therapeutic target that mediates morphine-induced cardioprotection. We also provide evidence suggesting that the activation of spinal NOS signaling is essential for morphine cardioprotection.
Map position and genomic organization of the kps cluster for polysialic acid synthesis in Escherichia coli K1

The multigenic kps cluster in Escherichia coli K1 encodes functions for synthesis of a polysialic acid capsule. DNA probes flanking each side of the cluster were hybridized to lambda clones bearing overlapping E. coli W3110 genomic fragments. These fragments covered the region between 60 and 70 map units on the chromosome. The results located kps to an accretion domain near 64 map units and established the orientation of kps cluster genes. Acquisition of kps by the E. coli genome was apparently the result of an ancestral transpositionlike addition event.
Increased NADPH-Oxidase Activity and Nox4 Expression During Chronic Hypertension Is Associated With Enhanced Cerebral Vasodilatation to NADPH In Vivo

Background and Purpose— We examined the importance of NADPH-oxidase in reactive oxygen species production in cerebral arteries and its effect on vascular tone in vivo. Furthermore, we investigated whether chronic hypertension affects function or expression of this enzyme in cerebral vessels. Methods— Superoxide generation was detected in isolated rat basilar arteries with the use of lucigenin-enhanced chemiluminescence. mRNA expression of NADPH-oxidase subunits was assessed by real-time polymerase chain reaction. Basilar artery diameter was measured with the use of a cranial window preparation in anesthetized rats. Results— NADPH-stimulated superoxide production was 2.3-fold higher in arteries from spontaneously hypertensive rats (SHR) versus normotensive Wistar-Kyoto rats (WKY) and could be blocked by the NADPH-oxidase inhibitor diphenyleneiodonium. Higher NADPH-oxidase activity was also reflected at the molecular level as mRNA expression of the NADPH-oxidase subunit Nox4 was 4.1-fold higher in basilar arteries from SHR versus WKY. In contrast, expression of Nox1, gp91phox, p22phox, and p47phox did not differ between strains. Application of NADPH to basilar arteries caused larger vasodilatation in SHR than WKY. Vasodilatation to NADPH could be attenuated by diphenyleneiodonium, as well as diethyldithiocarbamate (Cu2+/Zn2+–superoxide dismutase inhibitor), catalase (H2O2 scavenger), or tetraethylammonium (BKCa channel inhibitor). Conclusions— Activation of NADPH-oxidase in cerebral arteries generates superoxide, which is dismutated by Cu2+/Zn2+–superoxide dismutase to H2O2. H2O2 then elicits vasodilatation via activation of BKCa channels. Upregulation of Nox4 during chronic hypertension is associated with elevated cerebral artery NADPH-oxidase activity.
Effects of lamotrigine on PCP-evoked elevations in monoamine levels in the medial prefrontal cortex of freely moving rats

Lamotrigine is suggested to have potential as an add-on treatment for patients with schizophrenia. Supporting evidence comes from the efficacy of the drug in models of psychotic-like behaviour induced by N-methyl-D-aspartate (NMDA) receptor antagonists, such as phencyclidine (PCP). These drugs enhance levels of the monoamines in the cortex, which may contribute to their psychotomimetic effects. The ability of lamotrigine to prevent these neurochemical changes has not been examined. We studied PCP-evoked overflow of noradrenaline, dopamine and serotonin in the medial prefrontal cortex of awake rats using microdialysis. Rats were administered lamotrigine or vehicle, followed by PCP. Locomotor activity was also recorded before and after drug treatment. Lamotrigine did not have an influence on basal levels of the monoamines, but significantly reduced PCP-evoked overflow of dopamine and serotonin; PCP-evoked overflow of noradrenaline was also reduced by lamotrigine, but not to a significant degree. In contrast, PCP-induced hyperactivity was unaffected by lamotrigine. It is concluded that lamotrigine can modify PCP-evoked monoamine overflow in the cortex, consistent with an ability to prevent the psychotomimetic effects of NMDA receptor antagonists in rodents and humans. The dissociation between monoamine overflow and locomotor activity suggests the involvement of different brain circuits; relevance to the treatment of schizophrenia is also discussed.
Clonal haematopoiesis in children with acquired aplastic anaemia

Summary. The methylation pattern of three X‐linked genes, phosphoglycerate kinase (PGK), hypoxanthine phosphoribosyl transferase (HPRT) and DXS255 detected by hypervariable M27β probe, was analysed to determine the proportion of aplastic anaemia (AA) with clonal haematopoiesis in Japanese children. Methylation analysis was performed on DNA from separated granulocytes and compared to that of bone marrow derived fibroblasts to exclude selective lyonization in all somatic cells. Of 20 female patients examined, the methylation pattern of at least one gene was informative in granulocyte DNA from 18 patients (90%). Of these, 8/20 patients (40%) were heterozygous for PGK, 8/18 (44%) were heterozygous for HPRT and 17/18 (94%) were heterozygous for DXS255. In 14/18 patients both alleles were equally methylated. Four patients exhibited a unilateral methylation pattern in their granulocytes. The same unilateral pattern was again demonstrated in fibroblasts from two of the four patients suggesting that in the latter one X chromosome was selectively inactivated in all of the somatic cells. The remaining two patients showed a unilateral methylation pattern that was restricted to their granulocytes, suggesting the existence of true clonal haematopoiesis. They responded well to antilymphocyte globulin (ALG) and presently have no evidence of a clonal disorder such as myelodysplastic syndrome (MDS) or paroxysmal nocturnal haemoglobinuria (PNH). Although these results indicate that some children with AA exhibit clonal haematopoiesis, analysis of a greater number of subjects will be required to establish the clinical value of clonal haematopoiesis in patients with AA.
Anxiety as a predictor of response to interpersonal psychotherapy for recurrent major depression: An exploratory investigation

Major depression and anxiety frequently co‐occur, but the implications for psychological treatments have rarely been studied. We examined predictors of acute response to interpersonal psychotherapy in 134 consecutively treated female outpatients with recurrent unipolar depression. Women who failed to remit with interpersonal psychotherapy alone experienced higher levels of somatic anxiety, were more likely to meet criteria for lifetime panic disorder, were more likely to meet criteria for nonendogenous or nonmelancholic depression, and reported greater vocational impairment, higher levels of global severity, a longer duration of the index episode, and, somewhat surprisingly, lower levels of social impairment at pretreatment evaluation. A series of backwards stepping logistic regression analyses showed higher levels of baseline somatic anxiety and social functioning to be the most consistent predictors of nonresponse. Our findings strengthen existing evidence that concomitant anxiety can adversely affect the outcome of interpersonal therapy for depression. Depression and Anxiety 8:135–141, 1998. © 1998 Wiley‐Liss, Inc.
Parameterized Algorithms on Perfect Graphs for deletion to (r, ℓ)-graphs

For fixed integers $r,\ell \geq 0$, a graph $G$ is called an {\em $(r,\ell)$-graph} if the vertex set $V(G)$ can be partitioned into $r$ independent sets and $\ell$ cliques. The class of $(r, \ell)$ graphs generalizes $r$-colourable graphs (when $\ell =0)$ and hence not surprisingly, determining whether a given graph is an $(r, \ell)$-graph is \NP-hard even when $r \geq 3$ or $\ell \geq 3$ in general graphs. When $r$ and $\ell$ are part of the input, then the recognition problem is NP-hard even if the input graph is a perfect graph (where the {\sc Chromatic Number} problem is solvable in polynomial time). It is also known to be fixed-parameter tractable (FPT) on perfect graphs when parameterized by $r$ and $\ell$. I.e. there is an $f(r+\ell) \cdot n^{\Oh(1)}$ algorithm on perfect graphs on $n$ vertices where $f$ is some (exponential) function of $r$ and $\ell$. In this paper, we consider the parameterized complexity of the following problem, which we call {\sc Vertex Partization}. Given a perfect graph $G$ and positive integers $r,\ell,k$ decide whether there exists a set $S\subseteq V(G)$ of size at most $k$ such that the deletion of $S$ from $G$ results in an $(r,\ell)$-graph. We obtain the following results: \begin{enumerate} \item {\sc Vertex Partization} on perfect graphs is FPT when parameterized by $k+r+\ell$. \item The problem does not admit any polynomial sized kernel when parameterized by $k+r+\ell$. In other words, in polynomial time, the input graph can not be compressed to an equivalent instance of size polynomial in $k+r+\ell$. In fact, our result holds even when $k=0$. \item When $r,\ell$ are universal constants, then {\sc Vertex Partization} on perfect graphs, parameterized by $k$, has a polynomial sized kernel. \end{enumerate}
Congenital malformations in twins.

Among 1195 twins born in the Collaborative Perinatal Project, for whom information was available, 219 (18.33%) were found to have malformations, 179 (14.98%) single and 40 (3.35%,) multiple. The fre quency of malformations among twins was significantly higher than that among singletons from the same population, but the difference was entirely contributed by MZ twins. This holds true for both major and minor malformations. The frequency among Negro twins was higher than among white, and among male twins higher than among female. Twins had more malformations of the central nervous, musculo skeletal, ear, respiratory, cardiovascular, and alimentary systems and fewer malformations of the genito urinary and integumentary systems than singletons. In a significant number of cases when one twin of a pair had a malformation, the cotwin also had a ma/formation though not necessarily the same as that of the first twin. The Collaborative Study of Cerebral Palsy, Mental Retardation, and Other Neurological and Sensory Disorders of Infancy and Childhood is supported by the National Institute of Neurological and Communicative Dis orders and Stroke. The following institutions participate: Boston Lying-in Hospital; Brown University; Charity Hospital, New Orleans; Children's Hospital of Buffalo; Children's Hospital of Philadelphia; Chil dren's Medical Center, Boston; Columbia University; Johns Hopkins University; Medical College of Virginia; New York Medical College; Pennsylvania Hospital; University of Minnesota; University of Oregon; University of Tennessee and the Perinatal Research Branch, NINCDS. This report is based on data from twins born in the Collaborative Perinatal Project of the United States. As mentioned in a previous paper, this is a prospective study of factors which affect the parents before and during pregnancy and their relation to the outcome of pregnancy. Among 56,249 pregnancies with known outcomes 615 pairs of twins were born, 259 pairs to white mothers, 331 pairs to Negro mothers, and 25 pairs to mothers of " Other " ethnic groups, mostly Puerto Rican. The zygosity of 508 pairs was established by comparison of sex, blood types utilizing nine systems
Exposure to the JNK inhibitor SP600125 (anthrapyrazolone) during early zebrafish development results in morphological defects

SP600125 (anthrapyrazolone) is a synthetic polyaromatic chemical that inhibits c‐Jun N‐terminal kinase (JNK) signaling by interfering with phosphorylation of c‐Jun. To determine the pharmacological impact of SP600125 on zebrafish development, we incubated embryos in various concentrations of SP600125 from 18 h postfertilization (hpf) to 48 hpf. Embryos treated with 1.25 µm appeared with occasional pericardium edema. Treatment with 12.5 µm resulted in complete mortality by 120 hpf, preventing an assessment of physiological defects. Embryos treated with 5 µm exhibited slowed overall growth, a delay in hatching and numerous morphological defects such as pericardium edema, yolk sac edema, swim bladder deflation, bent vertebrae and eye and jaw malformations. Whole‐mount immunohistochemical studies using an anti‐acetylated β‐tubulin antibody confirmed developmental defects in the nervous system. Within the retina, fish treated with 1.25 µm showed a mild reduction of immunoreactivity. Immunoreactivity in the retina was further reduced in fish treated with 5 µm of SP600125. In these fish, eyes and olfactory organs were half the size compared with other groups. Multiple lenses were observed in 67% of these fish. A second experiment with a shorter exposure period of SP600125 (6 h) presented significantly fewer morphological defects. The treatment led to a delay in hatching, and increased incidences of swim bladder deflation and pericardium edema with increasing concentrations. In summary, SP600125 caused developmental abnormalities during zebrafish organogenesis starting at 1.25 µm and the defects were exacerbated with increasing concentrations. Our study suggests that SP600125 at 1.25 µm and beyond has devastating consequences for zebrafish development. Copyright © 2011 John Wiley & Sons, Ltd.
Asymptotic Density of Zimin Words

Word $W$ is an instance of word $V$ provided there is a homomorphism $\phi$ mapping letters to nonempty words so that $\phi(V) = W$. For example, taking $\phi$ such that $\phi(c)=fr$, $\phi(o)=e$ and $\phi(l)=zer$, we see that "freezer" is an instance of "cool". Let $\mathbb{I}_n(V,[q])$ be the probability that a random length $n$ word on the alphabet $[q] = \{1,2,\cdots q\}$ is an instance of $V$. Having previously shown that $\lim_{n \rightarrow \infty} \mathbb{I}_n(V,[q])$ exists, we now calculate this limit for two Zimin words, $Z_2 = aba$ and $Z_3 = abacaba$.
Product Classification in E-Commerce using Distributional Semantics

Product classification is the task of automatically predicting a taxonomy path for a product in a predefined taxonomy hierarchy given a textual product description or title. For efficient product classification we require a suitable representation for a document (the textual description of a product) feature vector and efficient and fast algorithms for prediction.To address the above challenges, we propose a new distributional semantics representation for document vector formation. We also develop a new two-level ensemble approach utilising (with respect to the taxonomy tree) path-wise, node-wise and depth-wise classifiers to reduce error in the final product classification task. Our experiments show the effectiveness of the distributional representation and the ensemble approach on data sets from a leading e-commerce platform and achieve improved results on various evaluation metrics compared to earlier approaches.
Acute Systemic Inflammation Increases Arterial Stiffness and Decreases Wave Reflections in Healthy Individuals

Background— Aortic stiffness is a marker of cardiovascular disease and an independent predictor of cardiovascular risk. Although an association between inflammatory markers and increased arterial stiffness has been suggested, the causative relationship between inflammation and arterial stiffness has not been investigated. Methods and Results— One hundred healthy individuals were studied according to a randomized, double-blind, sham procedure-controlled design. Each substudy consisted of 2 treatment arms, 1 with Salmonella typhi vaccination and 1 with sham vaccination. Vaccination produced a significant (P<0.01) increase in pulse wave velocity (at 8 hours by 0.43 m/s), denoting an increase in aortic stiffness. Wave reflections were reduced significantly (P<0.01) by vaccination (decrease in augmentation index of 5.0% at 8 hours and 2.5% at 32 hours) as a result of peripheral vasodilatation. These effects were associated with significant increases in inflammatory markers such as high-sensitivity C-reactive protein (P<0.001), high-sensitivity interleukin-6 (P<0.001), and matrix metalloproteinase-9 (P<0.01). With aspirin pretreatment (1200 mg PO), neither pulse wave velocity nor augmentation index changed significantly after vaccination (increase of 0.11 m/s and 0.4%, respectively; P=NS for both). Conclusions— This is the first study to show through a cause-and-effect relationship that acute systemic inflammation leads to deterioration of large-artery stiffness and to a decrease in wave reflections. These findings have important implications, given the importance of aortic stiffness for cardiovascular function and risk and the potential of therapeutic interventions with antiinflammatory properties.
An Efficient and Flexible Format for Linguistic and Semantic Annotation

The paper describes an XML annotation format and tool developed within the MUCHMORE project. The annotation scheme was designed specifically for the purposes of Cross-Lingual Information Retrieval in the medical domain so as to allow both efficient and flexible access to layers of information. We use a parallel English-German corpus of medical abstracts and annotate it with linguistic information (tokenisation, part-of-speech tagging, lemmatisation and decomposition, phrase recognition, grammatical functions) as well as semantic information from various sources. The annotation of medical terms/concepts, semantic types and semantic relations is based on the Unified Medical Language System (UMLS). Additionally, we use EuroWordNet as a general-language resource in annotating word senses and to compare domain-specific and general language use. A major aim of the project is also to complement existing ontological resources by extracting new terms and new semantic relations. We present the annotation scheme, which is conceptually related to stand-off annotation, and describe our tool for automatic semantic annotation.