Miracle-dz/UniFAR-FTUs huggingface dataset:
First molecular characterization of Cryptosporidium in Yemen

SUMMARY Cryptosporidium is a protozoan parasite of humans and animals and has a worldwide distribution. The parasite has a unique epidemiology in Middle Eastern countries where the IId subtype family of Cryptosporidium parvum dominates. However, there has been no information on Cryptosporidium species in Yemen. Thus, this study was conducted in Yemen to examine the distribution of Cryptosporidium species and subtype families. Fecal samples were collected from 335 patients who attended hospitals in Sana'a city. Cryptosporidium species were determined by PCR and sequence analysis of the 18 s rRNA gene. Cryptosporidium parvum and C. hominis subtypes were identified based on sequence analysis of the 60 kDa glycoprotein (gp60) gene. Out of 335 samples, 33 (9·9%) were positive for Cryptosporidium. Of them, 97% were identified as C. parvum whilst 1 case (3%) was caused by C. hominis. All 7 C. parvum isolates subtyped belonged to the IIaA15G2R1 subtype. The common occurrence of the zoonotic IIa subtype family of C. parvum highlights the potential occurrence of zoonotic transmission of cryptosporidiosis in Yemen. However, this postulation needs confirmation with future molecular epidemiological studies of cryptosporidiosis in both humans and animals in Yemen.
A Statistical Perspective on Randomized Sketching for Ordinary Least-Squares

We consider statistical as well as algorithmic aspects of solving large-scale least-squares (LS) problems using randomized sketching algorithms. For a LS problem with input data $(X, Y) \in \mathbb{R}^{n \times p} \times \mathbb{R}^n$, sketching algorithms use a sketching matrix, $S\in\mathbb{R}^{r \times n}$ with $r \ll n$. Then, rather than solving the LS problem using the full data $(X,Y)$, sketching algorithms solve the LS problem using only the sketched data $(SX, SY)$. Prior work has typically adopted an algorithmic perspective, in that it has made no statistical assumptions on the input $X$ and $Y$, and instead it has been assumed that the data $(X,Y)$ are fixed and worst-case (WC). Prior results show that, when using sketching matrices such as random projections and leverage-score sampling algorithms, with $p < r \ll n$, the WC error is the same as solving the original problem, up to a small constant. From a statistical perspective, we typically consider the mean-squared error performance of randomized sketching algorithms, when data $(X, Y)$ are generated according to a statistical model $Y = X \beta + \epsilon$, where $\epsilon$ is a noise process. We provide a rigorous comparison of both perspectives leading to insights on how they differ. To do this, we first develop a framework for assessing algorithmic and statistical aspects of randomized sketching methods. We then consider the statistical prediction efficiency (PE) and the statistical residual efficiency (RE) of the sketched LS estimator; and we use our framework to provide upper bounds for several types of random projection and random sampling sketching algorithms. Among other results, we show that the RE can be upper bounded when $p < r \ll n$ while the PE typically requires the sample size $r$ to be substantially larger. Lower bounds developed in subsequent results show that our upper bounds on PE can not be improved.
Determinants of compliance to iron supplementation among pregnant women in Enugu, Southeastern Nigeria.

BACKGROUND Anemia in pregnancy is highly prevalent among antenatal clinic attendees in Enugu, Nigeria despite the practice of routine iron supplementation in pregnancy. The major problem with iron supplementation in pregnancy is compliance, and this may be a potential driver to the persistent high prevalence of anemia in this population. OBJECTIVES To find out the compliance rate and determinants of compliance to iron supplementation among pregnant women in Enugu, southeastern Nigeria. MATERIALS AND METHODS This was a questionnaire-based cross-sectional study of eligible pregnant women receiving antenatal care at the University of Nigeria Teaching Hospital (UNTH), Ituku/Ozalla, Enugu, Nigeria between April 1, 2012 and January 31, 2013. RESULTS The knowledge of iron supplementation was 76.3% ( n = 302), however, the compliance rate was 65.9% ( n = 261). Tertiary level of education and high social class were factors significantly associated with compliance to iron supplementation after adjusting for other factors in the binary logistic regression analysis ( P < 0.05). The major barriers to compliance to iron supplementation included gastrointestinal side effects of iron supplements (41.7%), non-affordability of iron supplements (28.3%), and forgetfulness (15.0%) among the antenatal mothers. CONCLUSION The compliance rate of 65.9% for iron supplementation by pregnant mothers in Enugu can further be improved by providing the drug free of charge in the short term and improvement in education and socioeconomic class of the populace in the long run.
Vascular Biomarkers in the Prediction of Clinical Cardiovascular Disease: The Strong Heart Study

We compared the ability of separately measured intimal-medial thickness and atherosclerotic plaque to predict incident cardiovascular disease. American Indian men and women from the Strong Heart Study who were free of cardiovascular disease were evaluated with carotid ultrasound and cardiovascular disease risk factor assessment. End-diastolic intimal-medial thickness of the common carotid arteries was measured and averaged. Arterial mass (cross-sectional area) was calculated from intimal-medial thickness and end-diastolic diameter. Atherosclerosis was defined by focal plaque (discrete thickening >50% relative to the adjacent wall) and the number of carotid segments containing plaque (plaque score); 2441 participants (age 63±8 years) were followed-up for a mean of 7.7±2.8 years, during which time 495 experienced incident cardiovascular disease events. Time-to-event analyses were performed in groups stratified according to diabetes and hypertension status. Cardiovascular disease events were predicted by presence and extent of atherosclerosis in all groups; intima-medial thickness and arterial mass were only associated with outcomes when neither hypertension nor diabetes was present. Unequivocal evidence of atherosclerosis (plaque) and its extent (plaque score) are independently associated with incident cardiovascular disease events in individuals without preexisting cardiovascular disease regardless of diabetes and hypertension status. Hypertension-related increases in intima-media thickness and arterial mass appear to limit their use as measures of early or diffuse atherosclerosis and, hence, association with cardiovascular disease outcomes. These findings support the utility of separate assessment of focal atherosclerosis and intimal-medial thickness in epidemiological studies, trials, and risk stratification protocols.
Phrase detectives: Utilizing collective intelligence for internet-scale language resource creation

We are witnessing a paradigm shift in Human Language Technology (HLT) that may well have an impact on the field comparable to the statistical revolution: acquiring large-scale resources by exploiting collective intelligence. An illustration of this new approach is Phrase Detectives, an interactive online game with a purpose for creating anaphorically annotated resources that makes use of a highly distributed population of contributors with different levels of expertise. The purpose of this article is to first of all give an overview of all aspects of Phrase Detectives, from the design of the game and the HLT methods we used to the results we have obtained so far. It furthermore summarizes the lessons that we have learned in developing this game which should help other researchers to design and implement similar games.
Trauma exposure interacts with impulsivity in predicting emotion regulation and depressive mood

Background Traumatic exposure may modulate the expression of impulsive behavioral dispositions and change the implementation of emotion regulation strategies associated with depressive mood. Past studies resulted in only limited comprehension of these relationships, especially because they failed to consider impulsivity as a multifactorial construct. Objective Based on Whiteside and Lynam's multidimensional model that identifies four distinct dispositional facets of impulsive-like behaviors, namely urgency, (lack of) premeditation, (lack of) perseverance, and sensation seeking (UPPS), the current study used a sample of community volunteers to investigate whether an interaction exists between impulsivity facets and lifetime trauma exposure in predicting cognitive emotion regulation and depressive mood. Methods Ninety-three adults completed questionnaires measuring lifetime trauma exposure, impulsivity, cognitive emotion regulation, and depressive mood. Results Results showed that trauma-exposed participants with a strong disposition toward urgency (predisposition to act rashly in intense emotional contexts) tended to use fewer appropriate cognitive emotion regulation strategies than other individuals. Unexpectedly, participants lacking in perseverance (predisposition to have difficulties concentrating on demanding tasks) used more appropriate emotion regulation strategies if they had experienced traumatic events during their life than if they had not. Emotion regulation mediated the path between these two impulsivity facets and depressive mood. Conclusions Together, these findings suggest that impulsivity has a differential impact on emotion regulation and depressive mood depending on lifetime exposure to environmental factors, especially traumatic events.
Micro teleoperation with parallel manipulator

In this paper, we discuss about micro teleoperation with haptic interfaces. We developed the micro teleoperation systems for micro tasks, such as assembly or manufacturing. We show about structure of master/slave manipulators, its control and experimental results of teleoperation with the manipulators in this paper. We introduce the haptic interface that provides operators the sense as if he/she touches the expanded micro objects with his/her fingers. This micro tele-manipulation system is a new tool, which enables human operators to touch and feel the expanded micro objects with their fingers.
Rubber-like Exaggeration for Character Animation

Motion capture cannot generate cartoon-style animation directly. We emulate the rubber-like exaggerations common in traditional character animation as a means of converting motion capture data into cartoon-like movement. We achieve this using trajectory-based motion exaggeration while allowing the violation of link-length constraints. We extend this technique to obtain smooth, rubber-like motion by dividing the original links into shorter sub-links and computing the positions of joints using B´ezier curve interpolation and a mass-spring simulation. This method is fast enough to be used in real time.
Ceapins inhibit ATF6α signaling by selectively preventing transport of ATF6α to the Golgi apparatus during ER stress

The membrane-bound transcription factor ATF6α is activated by proteolysis during endoplasmic reticulum (ER) stress. ATF6α target genes encode foldases, chaperones, and lipid biosynthesis enzymes that increase protein-folding capacity in response to demand. The off-state of ATF6α is maintained by its spatial separation in the ER from Golgi-resident proteases that activate it. ER stress induces trafficking of ATF6α. We discovered Ceapins, a class of pyrazole amides, as selective inhibitors of ATF6α signaling that do not inhibit the Golgi proteases or other UPR branches. We show that Ceapins block ATF6α signaling by trapping it in ER-resident foci that are excluded from ER exit sites. Removing the requirement for trafficking by pharmacological elimination of the spatial separation of the ER and Golgi apparatus restored cleavage of ATF6α in the presence of Ceapins. Washout of Ceapins resensitized ATF6α to ER stress. These results suggest that trafficking of ATF6α is regulated by its oligomeric state. DOI: http://dx.doi. org/10.7554/eLife.11880. 001
New Herbicide Strategies for Weed Management in Pumpkin and Soybean and Potato Vine Desiccation

Weed control and desiccation are routinely executed with herbicides. Potato vine desiccation facilitates harvest, improves skin set, and regulates tuber size. Saflufenacil, glufosinate, saflufenacil plus glufosinate, and carfentrazone plus glufosinate were compared to diquat applied at 43, 31, and 17% B potatoes; similar vine desiccation (14 days after treatment), skin set, and yield were noted amongst treatments. Residual herbicides are routinely used for weed control in pumpkin. Fluridone and acetochlor formulations applied preemergence were evaluated in direct-seeded pumpkin compared to other labeled herbicides. Fluridone resulted in total crop loss following heavy rainfall immediately after planting; less rainfall resulted in transient injury. Acetochlor formulations resulted in significant pumpkin injury (34 to 39%) 14 days after planting. Smetolachlor controlled weeds similar to acetochlor without significant injury. Palmer amaranth has developed resistance to six different herbicide modes of action. The weed grows rapidly and is best controlled <10 cm in height. To control glyphosate and ALSresistant biotypes, fomesafen plus dicamba were applied at first postemergence (POST) to small Palmer amaranth (<5 cm, 0 d) and at simulated delays of 7, 14, 21, and 28 d. All plots received lactofen plus dicamba 14 days after first POST. Palmer amaranth control 14 days after first POST was 100% when delayed 0 or 7 d and 62% at the 28 day delay; control increased to 88% following lactofen plus dicamba applied second POST. Yield was significantly reduced when first POST was delayed 28 days at one location.
Clean Time-Dependent String Backgrounds from Bubble Baths

We consider the set of controlled time-dependent backgrounds of general relativity and string theory describing `bubbles of nothing', obtained via double analytic continuation of black hole solutions. We analyze their quantum stability, uncover some novel features of their dynamics, identify their causal structure and observables, and compute their particle production spectrum. We present a general relation between squeezed states, such as those arising in cosmological particle creation, and nonlocal theories on the string worldsheet. The bubble backgrounds have various aspects in common with de Sitter space, Rindler space, and moving mirror systems, but constitute controlled solutions of general relativity and string theory with no external forces. They provide a useful theoretical laboratory for studying issues of observables in systems with cosmological horizons, particle creation, and time-dependent string perturbation theory.
Differential expression of myometrial AP‐1 proteins during gestation and labour

Preterm labour (PTL) is a leading cause of perinatal mortality and postnatal morbidity. Contractions of the uterine muscle (myometrium) that determine the onset of labour depend on the expression of contraction‐associated proteins (CAPs, i.e. connexin43) regulated by dimeric AP‐1 transcription factors. Here, we examined subcellular (by immunoblotting) and tissue expression (by immunohistochemistry) of myometrial AP‐1 proteins (cJUN, JUNB, JUND, cFOS, FOSB, FRA1, FRA2) throughout gestation and TL in different species (mouse, rat and human). To identify the critical AP‐1 members associated with preterm birth, we studied their expression in mouse model of ‘infectious’ (LPS‐induced) and ‘sterile’ (RU486‐induced) PTL. We found that (1) myometrial AP‐1 composition is preserved in vivo between different species (rodents and human) indicating that Fos/Jun heterodimer (i.e. FRA2/JUND) may be indispensable for labour initiation. (2) Our in vivo study using murine models of gestation shows that there is a similarity in the myometrial AP‐1 protein composition during TL and pathological PTL of different aetiology suggesting the involvement of similar molecular machinery in the induction of labour. (3) This study is first comprehensive protein analysis of seven AP‐1 members in human labouring versus non‐labouring myometrium, showing their cellular expression and tissue distribution in relation to labour status.
Inhibition of CD39 Enzymatic Function at the Surface of Tumor Cells Alleviates Their Immunosuppressive Activity

Bastid and colleagues show that CD39 is highly expressed on tumor-infiltrating lymphocytes, tumor stroma, but also on tumor cells; treatment with CD39 inhibitors or blocking antibody alleviated the tumor-induced inhibition of T-cell proliferation and increased CTL- and NK cell–mediated cytotoxicity. The ectonucleotidases CD39 and CD73 hydrolyze extracellular adenosine triphosphate (ATP) and adenosine diphosphate (ADP) to generate adenosine, which binds to adenosine receptors and inhibits T-cell and natural killer (NK)–cell responses, thereby suppressing the immune system. The generation of adenosine via the CD39/CD73 pathway is recognized as a major mechanism of regulatory T cell (Treg) immunosuppressive function. The number of CD39+ Tregs is increased in some human cancers, and the importance of CD39+ Tregs in promoting tumor growth and metastasis has been demonstrated using several in vivo models. Here, we addressed whether CD39 is expressed by tumor cells and whether CD39+ tumor cells mediate immunosuppression via the adenosine pathway. Immunohistochemical staining of normal and tumor tissues revealed that CD39 expression is significantly higher in several types of human cancer than in normal tissues. In cancer specimens, CD39 is expressed by infiltrating lymphocytes, the tumor stroma, and tumor cells. Furthermore, the expression of CD39 at the cell surface of tumor cells was directly demonstrated via flow cytometry of human cancer cell lines. CD39 in cancer cells displays ATPase activity and, together with CD73, generates adenosine. CD39+CD73+ cancer cells inhibited the proliferation of CD4 and CD8 T cells and the generation of cytotoxic effector CD8 T cells (CTL) in a CD39- and adenosine-dependent manner. Treatment with a CD39 inhibitor or blocking antibody alleviated the tumor-induced inhibition of CD4 and CD8 T-cell proliferation and increased CTL- and NK cell–mediated cytotoxicity. In conclusion, interfering with the CD39–adenosine pathway may represent a novel immunotherapeutic strategy for inhibiting tumor cell–mediated immunosuppression. Cancer Immunol Res; 3(3); 254–65. ©2014 AACR.
Mean Square Convergence of Consensus Algorithms in Random WSNs

Distributed consensus algorithms for estimation of parameters or detection of events in wireless sensor networks have attracted considerable attention in recent years. A necessary condition to achieve a consensus on the average of the initial values is that the topology of the underlying graph is balanced or symmetric at every time instant. However, communication impairments can make the topology vary randomly in time, and instantaneous link symmetry between pairs of nodes is not guaranteed unless an acknowledgment protocol or an equivalent approach is implemented. In this paper, we evaluate the convergence of the consensus algorithm in the mean square sense in wireless sensor networks with random asymmetric topologies. For the case of links with equal probability of connection, a closed form expression for the mean square error of the state along with the dynamical range and the optimum value of the link weights that guarantee convergence are derived. For the case of links with different probabilities of connection, an upper bound for the mean square error of the state is derived. This upper bound can be computed for any time instant and can be employed to compute a link weight that reduces the convergence time of the algorithm.
Restriction-Modification Systems as Mobile Genetic Elements in the Evolution of an Intracellular Symbiont

Long-term vertical transmission of intracellular bacteria causes massive genomic erosion and results in extremely small genomes, particularly in ancient symbionts. Genome reduction is typically preceded by the accumulation of pseudogenes and proliferation of mobile genetic elements, which are responsible for chromosome rearrangements during the initial stage of endosymbiosis. We compared the genomes of an endosymbiont of termite gut flagellates, “Candidatus Endomicrobium trichonymphae,” and its free-living relative Endomicrobium proavitum and discovered many remnants of restriction-modification (R-M) systems that are consistently associated with genome rearrangements in the endosymbiont genome. The rearrangements include apparent insertions, transpositions, and the duplication of a genomic region; there was no evidence of transposon structures or other mobile elements. Our study reveals a so far unrecognized mechanism for genome rearrangements in intracellular symbionts and sheds new light on the general role of R-M systems in genome evolution.
Multifunctional fructans and raffinose family oligosaccharides

Fructans and raffinose family oligosaccharides (RFOs) are the two most important classes of water-soluble carbohydrates in plants. Recent progress is summarized on their metabolism (and regulation) and on their functions in plants and in food (prebiotics, antioxidants). Interest has shifted from the classic inulin-type fructans to more complex fructans. Similarly, alternative RFOs were discovered next to the classic RFOs. Considerable progress has been made in the understanding of structure–function relationships among different kinds of plant fructan metabolizing enzymes. This helps to understand their evolution from (invertase) ancestors, and the evolution and role of so-called “defective invertases. ” Both fructans and RFOs can act as reserve carbohydrates, membrane stabilizers and stress tolerance mediators. Fructan metabolism can also play a role in osmoregulation (e.g., flower opening) and source–sink relationships. Here, two novel emerging roles are highlighted. First, fructans and RFOs may contribute to overall cellular reactive oxygen species (ROS) homeostasis by specific ROS scavenging processes in the vicinity of organellar membranes (e.g., vacuole, chloroplasts). Second, it is hypothesized that small fructans and RFOs act as phloem-mobile signaling compounds under stress. It is speculated that such underlying antioxidant and oligosaccharide signaling mechanisms contribute to disease prevention in plants as well as in animals and in humans.
P53 Is Essential for Developmental Neuron Death as Regulated by the TrkA and p75 Neurotrophin Receptors

Naturally occurring sympathetic neuron death is the result of two apoptotic signaling events: one normally suppressed by NGF/TrkA survival signals, and a second activated by the p75 neurotrophin receptor. Here we demonstrate that the p53 tumor suppressor protein, likely as induced by the MEKK-JNK pathway, is an essential component of both of these apoptotic signaling cascades. In cultured neonatal sympathetic neurons, p53 protein levels are elevated in response to both NGF withdrawal and p75NTR activation. NGF withdrawal also results in elevation of a known p53 target, the apoptotic protein Bax. Functional ablation of p53 using the adenovirus E1B55K protein inhibits neuronal apoptosis as induced by either NGF withdrawal or p75 activation. Direct stimulation of the MEKK-JNK pathway using activated MEKK1 has similar effects; p53 and Bax are increased and the subsequent neuronal apoptosis can be rescued by E1B55K. Expression of p53 in sympathetic neurons indicates that p53 functions downstream of JNK and upstream of Bax. Finally, when p53 levels are reduced or absent in p53+/− or p53−/− mice, naturally occurring sympathetic neuron death is inhibited. Thus, p53 is an essential common component of two receptor-mediated signal transduction cascades that converge on the MEKK-JNK pathway to regulate the developmental death of sympathetic neurons.