Miracle-dz/UniFAR-FTUs huggingface dataset:
Single‐cell genomics: unravelling the genomes of unculturable microorganisms

Microbial genomics and related transcriptomics methods rely on culturing techniques to obtain enough DNA suitable for high‐throughput sequencing without resorting to DNA amplification techniques. A few microgram of DNA is needed for most common next‐generation sequencing methods. For transcriptome analysis, sufficient cDNA is needed to measure low abundance mRNA copies in the cell. However, the large majority of microbes on earth resist cultivation, hampering research into their relevant gene pool, ecological niche or industrial relevance. For example, many environmental or gut‐related species cannot be grown outside their natural habitat. Even if we isolate the metagenome or the metatranscriptome from these environments, this reveals only a fragmented sequence landscape that is difficult to assign to individual species. Although enrichment techniques or metatransciptome analysis of previously unculturable species have been shown to assist in directed culturing, e.g. of a Rikenella‐like bacterium (Bomar et al., 2011), the unravelling of a complex metagenome into its individual genomes and their organization is impossible using current technologies. A major challenge is the analysis of bacteria and other organisms living inside a complex matrix, like biofilms. Metagenome or transcriptome analysis of microorganisms has been described for biofilms consisting of a single species by scraping of the biofilm to obtain enough material (Holmes et al., 2006), but for multi‐species biofilms this method results in a metagenome or metatranscriptome dataset. The solution to these challenges may be the isolation and genomic analysis of unculturable single cells isolated from such environments. Here we describe in brief the state‐of‐the‐art in single‐cell microbial genomics.
More Fibrosis and Thrombotic Complications but Similar Expression Patterns of Markers for Coagulation and Inflammation in Symptomatic Plaques from DM2 Patients

Objective: One of the possible pathological mechanisms behind the increased vascular injury in diabetes mellitus type 2 (DM2) is the formation of advanced glycation end products (AGEs). The aim of this study was to investigate whether the presence of AGEs and specific markers for coagulation and inflammation in symptomatic atherosclerotic plaques from DM2 patients differs from plaques from nondiabetics. Methods and results: Carotid atherectomies were obtained from DM2 patients (n = 11) and controls without DM2 matched for age and other cardiovascular risk factors (n = 12) who were treated for symptomatic carotid artery stenosis. Plaques were graded according to the American Heart Association classification of lesions. More fibrosis and more thrombotic complications (p = 0.007) were observed in carotid atherectomies from DM2 patients. Percentages of immunostained smooth muscle cells and macrophages in the lesions, quantified planimetrically, did not differ between the two groups. No differences were found in the immunostaining for T cells, tissue factor (TF), endothelial protein C receptor (EPCR), nuclear factor κB, and the AGE carboxymethyllysine. Conclusions: These findings demonstrate that DM2 is associated with increased plaque complications; however, a local changed presence of AGEs, TF, and EPCR seems not to be involved in this end stage of atherosclerosis.
Automated Data Processing as an AI Planning Problem

NASA s vision for Earth Science is to build a "sensor web"; an adaptive array of heterogeneous satellites and other sensors that will track important events, such as storms, and provide real-time information about the state of the Earth to a wide variety of customers. Achieving his vision will require automation not only in the scheduling of the observations but also in the processing af tee resulting data. Ta address this need, we have developed a planner-based agent to automatically generate and execute data-flow programs to produce the requested data products. Data processing domains are substantially different from other planning domains that have been explored, and this has led us to substantially different choices in terms of representation and algorithms. We discuss some of these differences and discuss the approach we have adopted.
Safety of Rotavirus Vaccine in the NICU

BACKGROUND AND OBJECTIVE: Rotavirus vaccination is discouraged during hospitalization given concerns regarding live attenuated virus transmission, although recommended upon discharge. Infants should have vaccination initiated by 104 days of age or they become age-ineligible. Our institution believed the known risk of severe disease in unvaccinated infants outweighed the theoretical risk of transmission. We routinely administer RotaTeq (RV5) to age-eligible hospitalized infants on enteral feeds. The objective of this study was to determine the safety of RV5 vaccination among vaccinated (VI) and unvaccinated infants (UVI) within the NICU. METHODS: A retrospective review identified VI between 2008 and 2010, and UVI geographically located near VI within 15 days of vaccination. We screened for gastrointestinal symptoms among UVI by using an electronic medical record query (trigger tool) to identify infants with orders for bowel rest, abdominal imaging, and antibiotics. Trigger-positive infants had full chart review. RESULTS: Most VI (76%) were either asymptomatic (25% [24 of 96]) or symptomatic but unchanged from baseline (51% [49 of 96]) postvaccination. Although 24% of VI had clinical status changes postvaccination, none were directly attributed to RV5. Among 801 neighboring UVI, 10 (1.2%) had clinical status changes, none directly attributed to RV5, but mostly bacterial sepsis or preexisting gastrointestinal pathology. Two UVI underwent stool analysis; both negative for rotavirus. CONCLUSIONS: RV5 was well tolerated in hospitalized infants, with most postvaccination symptoms attributed to preexisting symptoms. UVI seemed to have a low risk of symptomatic transmission. Inpatient administration ensures that age-eligible infants are vaccinated regardless of hospital duration. Prospective evaluation of safety and transmissibility is needed.
Dynamics of intact immunoglobulin G explored by drift-tube ion-mobility mass spectrometry and molecular modeling.

Collision cross-sections (CCS) of immunoglobulins G1 and G4 have been determined using linear drift-tube ion-mobility mass spectrometry. Intact antibodies and Fc-hinge fragments present with a larger range of CCS than proteins of comparable size. This is rationalized with MD simulations, which indicate significant in vacuo dynamics between linked folded domains. The IgG4 subclass presents over a wider CCS range than the IgG1 subclass.
EFNS guideline on mild traumatic brain injury: report of an EFNS task force

In 1999, a Task Force on Mild Traumatic Brain Injury (MTBI) was set up under the auspices of the European Federation of Neurological Societies. Its aim was to propose an acceptable uniform nomenclature for MTBI and definition of MTBI, and to develop a set of rules to guide initial management with respect to ancillary investigations, hospital admission, observation and follow‐up.
The Impact of Personality Traits and Employee Work-Related Attitudes on Employee Performance with the Moderating Effect of Organizational Culture : The Case of Saudi Arabia

The present conceptual study attempts to contribute new knowledge to the existing literature of personality, work-related attitudes and employee performance. Particularly, the study highlights the several definitions of personality in the contemporary literature. Further, the impact of personality traits (the big five model) and work related attitudes on employee work performance, including their inter-relationships was further discussed in an exhaustive detail. The study hypothesized that personality traits and workrelated attitudes such as job involvement and organizational commitment have direct positive significant relationships with employee work performance, with the moderating effect of organizational culture in the Saudi Arabian context.
Measuring extractive institutions: colonial trade and price gaps in French Africa

A common explanation for current African underdevelopment is the extractive character of institutions established during the colonial period. Yet, since colonial extraction is hard to quantify, the magnitude of this phenomenon is still unclear. In this paper, I address this gap in the literature by focusing on monopsonistic colonial trade in French Africa. By using new archival data on export prices, I provide yearly-estimates of colonial extraction via trade, measured as the gap between actual prices that the colonial trading companies paid to African agricultural producers and prices that should have been paid in a counter-factual competitive market (i.e. world prices minus trade costs). The results show that African prices were about half than what they would have been in competitive markets. This suggests that colonial trade dynamics was characterized by a considerable amount of extraction.
The Quarterly Journal of Experimental Psychology Spatial Anxiety Relates to Spatial Abilities as a Function of Working Memory in Children

distribution in any form to anyone is expressly forbidden. The publisher does not give any warranty express or implied or make any representation that the contents will be complete or accurate or up to date. The accuracy of any instructions, formulae, and drug doses should be independently verified with primary sources. The publisher shall not be liable for any loss, actions, claims, proceedings, demand, or costs or damages whatsoever or howsoever caused arising directly or indirectly in connection with or arising out of the use of this material.
Contact stress distributions in a turbine disc dovetail type joint ‐ a comparison of photoelastic and finite element results

Two dimensional photoelastic frozen stress techniques were used to investigate the stress distributions of an axially loaded dovetail joint as is found in the design of some turbine blade-disc fixings. The internal stress distributions were obtained by the shear difference method and were compared to results obtained by using the finite element method. It was found that steep principal stress gradients were present immediately below the contact surfaces in the zone adjacent to the fillet radius of the dovetail fixing, which could be an important consideration in the fatigue strength of the joint. The finite element model used gave the same trends of stress as the photoelastic model, predicted higher peak principal stresses and did not exhibit the same detailed variations of stress distribution.
A Revised Interpersonal Circumplex Inventory of Children’s Social Goals

Motivational factors such as social goals are important features of developing social adjustment, and thus researchers studying social adjustment need psychometrically sound measures of social goals. A valid measure of social goals for English-speaking youth is lacking. Such a measure would increase understanding of children’s social adjustment and allow for testing developmental models of social goals and interpersonal functioning. The authors’ aim was to revise the Interpersonal Goals Inventory for Children (IGI-C) for an English-speaking sample and examine its validity. The revised IGI-C (IGI-CR) fit a circumplex model and performed as expected with most external criterion variables examined. In addition, some differences were observed across males and females, offering insights into gender differences in social goals. Results support the IGI-CR as a sound measure.
Plasma folate level and high-dose folate supplementation predict sulfadoxine-pyrimethamine treatment failure in pregnant women in Western kenya who have uncomplicated malaria.

UNLABELLED Sulfadoxine-pyrimethamine (SP) inhibits folate metabolism by the malaria parasite. We investigated the association between folate levels and SP failure in pregnant women. Data from a trial to assess the effect that folate supplementation has on SP failure in 467 pregnant women were analyzed. Plasma folate levels were determined at enrollment and at day 7. High baseline folate levels, high parasite densities, and age <20 years were risk factors for SP failure. High-dose (5 mg daily) folate supplementation or high folate levels at day 7 were independent risk factors. Therefore, pregnant women receiving SP should receive low-/moderate-dose folate supplementation. TRIAL REGISTRATION http://www.clinicaltrials. gov identifier: NCT00130065.
3D Visual Response Properties of MSTd Emerge from an Efficient, Sparse Population Code

Neurons in the dorsal subregion of the medial superior temporal (MSTd) area of the macaque respond to large, complex patterns of retinal flow, implying a role in the analysis of self-motion. Some neurons are selective for the expanding radial motion that occurs as an observer moves through the environment (“heading”), and computational models can account for this finding. However, ample evidence suggests that MSTd neurons exhibit a continuum of visual response selectivity to large-field motion stimuli. Furthermore, the underlying computational principles by which these response properties are derived remain poorly understood. Here we describe a computational model of macaque MSTd based on the hypothesis that neurons in MSTd efficiently encode the continuum of large-field retinal flow patterns on the basis of inputs received from neurons in MT with receptive fields that resemble basis vectors recovered with non-negative matrix factorization. These assumptions are sufficient to quantitatively simulate neurophysiological response properties of MSTd cells, such as 3D translation and rotation selectivity, suggesting that these properties might simply be a byproduct of MSTd neurons performing dimensionality reduction on their inputs. At the population level, model MSTd accurately predicts eye velocity and heading using a sparse distributed code, consistent with the idea that biological MSTd might be well equipped to efficiently encode various self-motion variables. The present work aims to add some structure to the often contradictory findings about macaque MSTd, and offers a biologically plausible account of a wide range of visual response properties ranging from single-unit selectivity to population statistics. SIGNIFICANCE STATEMENT Using a dimensionality reduction technique known as non-negative matrix factorization, we found that a variety of medial superior temporal (MSTd) neural response properties could be derived from MT-like input features. The responses that emerge from this technique, such as 3D translation and rotation selectivity, spiral tuning, and heading selectivity, can account for a number of empirical results. These findings (1) provide a further step toward a scientific understanding of the often nonintuitive response properties of MSTd neurons; (2) suggest that response properties, such as complex motion tuning and heading selectivity, might simply be a byproduct of MSTd neurons performing dimensionality reduction on their inputs; and (3) imply that motion perception in the cortex is consistent with ideas from the efficient-coding and free-energy principles.
Dislocations and Cracks in Anisotropic Elasticity

The solution of the elastic equations is considered for the case in which the state of the solid is independent of one of the three Cartesian coordinates. The stresses due to a dislocation, a wall of parallel dislocations, and a crack in an arbitrary non-uniform stress field are obtained. The results hold for the most general anisotropy in which no symmetry elements of the crystal are assumed.
Sustainability evaluation of software architectures: a systematic review

Long-living software systems are sustainable if they can be cost-efficiently maintained and evolved over their entire life-cycle. The quality of software architectures determines sustainability to a large extent. Scenario-based software architecture evaluation methods can support sustainability analysis, but they are still reluctantly used in practice. They are also not integrated with architecture-level metrics when evaluating implemented systems, which limits their capabilities. Existing literature reviews for architecture evaluation focus on scenario-based methods, but do not provide a critical reflection of the applicability of such methods for sustainability evaluation. Our goal is to measure the sustainability of a software architecture both during early design using scenarios and during evolution using scenarios and metrics, which is highly relevant in practice. We thus provide a systematic literature review assessing scenario-based methods for sustainability support and categorize more than 40 architecture-level metrics according to several design principles. Our review identifies a need for further empirical research, for the integration of existing methods, and for the more efficient use of formal architectural models.
False promises: e-business deployment in Wales' SME community

Purpose – This study aims to examine usage and deployment trends of e‐business technologies within the small and medium‐sized enterprise (SMEs) community in Wales, since the turn of the millennium. Analysis of prior surveys such as the Department of Trade and Industry and Federation of Small Business reveals poor adoption levels of basic information and communication technology deployment and minimal uptake of sophisticated technologies in comparison to other UK regions. Uptake of e‐business was assessed through a quantitative survey of SMEs and contrasted against prior studies undertaken within Wales since 2000 to identify trends and levels of adoption.Design/methodology/approach – The study is comprised of a survey of 500 SMEs including a representative population from diverse geographical and economic regions within Wales. The survey deployed a proportionately stratified and representative sampling technique, whereby two‐thirds of the enterprises selected were micro sized classified enterprises with no.
Effect of Hypercapnic Acidosis on Renal Function in the Newborn Rabbit

ABSTRACT. Anaesthetized mechanically ventilated newborn rabbits were exposed to different degrees of hypercapnia. One hour of normocapnia was used as a control period. Renal function studies demonstrated an increase in renal vascular resistance with a concomitant decrease in effective renal plasma flow in all hypercapnic animals, combined with a less pronounced decrease in glomerular filtration rate. Filtration fraction rose significantly. A decrease in systemic blood pressure was only observed when the PaCO2 exceeded 100 mm Hg combined with an arterial pH below or equal to 7.10. We conclude that normoxemic hypercapnia in the newborn rabbit leads to an increase in renal vascular resistance and suggest that the renal vasoconstriction predominates at the level of the efferent arteriole.
A New Principle for Information Storage in an Enzymatic Pathway Model

Strong experimental evidence indicates that protein kinase and phosphatase (KP) cycles are critical to both the induction and maintenance of activity-dependent modifications in neurons. However, their contribution to information storage remains controversial, despite impressive modeling efforts. For instance, plasticity models based on KP cycles do not account for the maintenance of plastic modifications. Moreover, bistable KP cycle models that display memory fail to capture essential features of information storage: rapid onset, bidirectional control, graded amplitude, and finite lifetimes. Here, we show in a biophysical model that upstream activation of KP cycles, a ubiquitous mechanism, is sufficient to provide information storage with realistic induction and maintenance properties: plastic modifications are rapid, bidirectional, and graded, with finite lifetimes that are compatible with animal and human memory. The maintenance of plastic modifications relies on negligible reaction rates in basal conditions and thus depends on enzyme nonlinearity and activation properties of the activity-dependent KP cycle. Moreover, we show that information coding and memory maintenance are robust to stochastic fluctuations inherent to the molecular nature of activity-dependent KP cycle operation. This model provides a new principle for information storage where plasticity and memory emerge from a single dynamic process whose rate is controlled by neuronal activity. This principle strongly departs from the long-standing view that memory reflects stable steady states in biological systems, and offers a new perspective on memory in animals and humans.
The Effect of In-Service Teacher Training on Student Learning of English as a Second Language

In-service teacher training aims to improve the supply of public education. A randomized experiment was conducted in Mexico to test whether teacher training could increase teacher efficiency in public secondary schools. After seven and a half months of exposure to a trained teacher, students improved their English. This paper explores two mechanisms through which training can affect student learning. First, trained teachers improved their English by 0.35 standard deviations in the short run. Teachers in the control group caught up with treatment teachers by the end of the school year in part because teachers in the treatment group reduced out-of-pocket expenditures to learn English in 53 percent. Second, teachers changed classroom practices by providing more opportunities for students to actively engage in learning. This evidence suggests that teacher training may be effective at improving student learning and that teacher incentives may play a role in mediating its effects.
Live Imaging of Synaptic Vesicle Release and Retrieval in Dopaminergic Neurons

Dopaminergic (DA) neurons represent <0.01% of neurons in the human brain, but are essential for normal neurological and psychiatric function. The majority of these neurons reside in the ventral midbrain, but they exert their profound influences on brain function through projections to both the cortex and the basal ganglia. These projections secrete dopamine from small clear synaptic vesicles (SVs) in axonal varicosities. DA signaling has unique spatial and temporal characteristics as compared to the fast, focal synaptic transmission of excitatory and inhibitory neurons. However, as with fast-acting neurotransmitters, DA SVs must be locally recycled for use following exocytosis. Little is known about these DA SV recycling properties and how they might impact efficacy of DA neurotransmission. Here we used the pH-sensitive fluorescent probe synaptopHluorin to investigate SV recycling in DA neurons and compared their properties to prototypical fast neurotransmitter synapses of the hippocampus. These measurements showed that DA SVs, like hippocampal SVs, have a resting pH of ∼5.6. However, compared to hippocampal neurons, DA neurons show limited depletion of the recycling pool of vesicles as the stimulus frequency is increased from 5 to 30 Hz. Additional measurements show that exocytosis rates at this frequency are comparable between hippocampal and DA neurons. Thus, limited vesicle depletion likely arises from a stimulus frequency-dependent acceleration of DA SV endocytosis or re-acidification. Our observations imply differential regulation of endocytic–exocytic balance in DA neurons. Finally, our assay can also be used to investigate the effects of genetic and chemical modulation of the SV cycle.