Miracle-dz/UniFAR-FTUs huggingface dataset:
The Green Bank Ammonia Survey: Observations of Hierarchical Dense Gas Structures in Cepheus-L1251

We use Green Bank Ammonia Survey observations of NH3 (1, 1) and (2, 2) emission with 32″ FWHM resolution from a ∼10 pc2 portion of the Cepheus-L1251 molecular cloud to identify hierarchical dense gas structures. Our dendrogram analysis of the NH3 data results in 22 top-level structures, which reside within 13 lower-level parent structures. The structures are compact and are spatially correlated with the highest H2 column density portions of the cloud. We also compare the ammonia data to a catalog of dense cores identified by higher-resolution (18.″2 FWHM) Herschel Space Observatory observations of dust continuum emission from Cepheus-L1251. Maps of kinetic gas temperature, velocity dispersion, and NH3 column density, derived from detailed modeling of the NH3 data, are used to investigate the stability and chemistry of the ammonia-identified and Herschel-identified structures. We show that the dust and dense gas in the structures have similar temperatures, with median Tdust and TK measurements of 11.7 ± 1.1 K and 10.3 ± 2.0 K, respectively. Based on a virial analysis, we find that the ammonia-identified structures are gravitationally dominated, yet may be in or near a state of virial equilibrium. Meanwhile, the majority of the Herschel-identified dense cores appear to be not bound by their own gravity and instead confined by external pressure. CCS (20 − 10) and HC5N emission from the region reveal broader line widths and centroid velocity offsets when compared to the NH3 (1, 1) emission in some cases, likely due to these carbon-based molecules tracing the turbulent outer layers of the dense cores.
Further aspects of Toxoplasma gondii elimination in the presence of metals

Toxoplasma gondii, the etiological agent of toxoplasmosis, infects nucleated cells and then resides and multiplies within a parasitophorous vacuole. For this purpose, the parasite secretes many virulence factors for the purpose of invading and subverting the host microbicidal defenses in order to facilitate its survival in the intracellular milieu. Essential metals are structural components of proteins and enzymes or cofactors of enzymatic reactions responsible for these parasitic survival mechanisms. However, an excess of non-essential or essential metals can lead to parasite death. Thus, infected host cells were incubated with 20 μM ZnCl2 in conjunction with 3 μMCdCl2 or HgCl2 for 12 h in order to investigate cellular events and organelle damage related to intracellular parasite death and elimination. In the presence of these metals, the tachyzoites undergo lipid uptake and transport impairment, functional and structural mitochondrial disorders, DNA condensation, and acidification of the parasitophorous vacuole, thus leading to parasite death. Additional research has suggested that lysosome-vacuole fusion was involved in parasite elimination since acid phosphatases were found inside the parasitophorous vacuole, and vacuoles containing parasites were also positive for autophagy. In conclusion, low concentrations of CdCl2, HgCl2, and ZnCl2 can cause damage to Toxoplasma gondii organelles, leading to loss of viability, organelle death, and elimination without causing toxic effects to host cells.
A Method for Predicting Vehicles Motion Based on Road Scene Reconstruction and Neural Networks in Real Time

The suggested method helps predicting vehicles movement in order to give the driver more time to react and avoid collisions on roads. The algorithm is dynamically modelling the road scene around the vehicle based on the data from the onboard camera. All moving objects are monitored and represented by the dynamic model on a 2D map. After analyzing every object’s movement, the algorithm predicts its possible behavior.
Cortical thickness and functional connectivity abnormality in chronic headache and low back pain patients

This study aims to characterize the psychological wellbeing of chronic headache (CH) patients, to identify cortical structural abnormalities and any associations of those abnormalities with resting state functional connectivity (rsFC), and to determine whether such rsFC abnormality is specific to CH patients. Compared with healthy controls (CONCH), CH patients suffered from mild depression, sleep disturbances, and relatively poor quality of life. CH patients also exhibited widespread cortical thickness (CT) abnormalities in left premotor (BA6), right primary somatosensory (S1) and right prefrontal (BA10) cortices, as well as in regions of default mode and executive control networks. Using cortical regions with thickness abnormality as seeds, we found cortical region pairs showed strengthened rsFC in CH patients. Using the same seeds, rsFC analysis from chronic low back pain (CLBP) patients and their controls (CONCLBP) identified abnormalities in non‐overlapping cortical region pairs. Direct comparison of rsFC between CH and CLBP patients revealed significantly differences in thirteen cortical region pairs, including the four identified in CH and CONCH comparison. Across all three groups (CH, CLBP and CON), the rsFC between left multisensory association area (BA39) and left posterior cingulate cortex (BA23) differed significantly. Eight regions showed CT abnormality in CLBP patients, two of which overlapped with those of CH patients. Our observations support the notion that CH and CLBP pain are pathological conditions, under which the brain develops distinct widespread structural and functional abnormalities. CH and CLBP groups share some similar structural abnormalities, but rsFC abnormalities in several cortical region pairs appear to be pathology‐specific. Hum Brain Mapp 38:1815–1832, 2017. © 2017 Wiley Periodicals, Inc.
Vitamin D requirements in infancy: a systematic review

Purpose of reviewNew evidence for recommendations for vitamin D supplementation in healthy infants based upon recent literature. Recent findingsRandomized controlled trials published since 2009 that related to vitamin D doses in infancy were reviewed. They do not provide any additional evidence that larger, more generous amounts of daily vitamin D beyond the customary recommended 400 IU daily dose, affect any significant outcome. Larger amounts may lead to serum 25 hydroxy vitamin D concentrations that have been reported to be potentially associated with adverse effects. SummaryThere are still many unanswered questions left, in particular whether or not more ‘generous’ amounts of vitamin D in infancy may improve long-term health outcomes such as prevention of osteoporosis, allergies, or cancer.
Optimizing the use of anti VEGF targeted therapies in patients with metastatic colorectal cancer: review of literature

Colorectal cancer is one of the most frequent forms of cancer both in men and women, and patients with metastatic disease are now being exposed to an increasing number of therapeutic agents to improve the survival outcomes. Vascular endothelial growth factor (VEGF) has o key role in the tumor growth and spreading. The approval of 4 agents that target angiogenic pathways in combination with standard chemotherapy improve overall and progression free survival and offer many opportunities to sequencing the treatment in patients with metastatic colorectal cancer (mCRC). However, the most effective strategy for the use of these agents remains unclear. This article presents an overview of the actual evidence for the use of agents that target angiogenesis in the treatment of mCRC.
Some aspects of the comparative pathology of oxygen toxicity in the retina.

(a) Effect of hyperoxia (b) Relation to other vessels (4) Mouse. 523 (c) Study by direct observation in the living eye (a). Eff . t.of. hypero.i. (d) Relationship to concentrations of oxygen (a) Effect of hyperoxia (e) Study of digest preparations (b) On transfer to air (f) Effect of vitamin E (c) Newborn mice: Hyperplasia of hyaloid vessels (g) Effect of returning to air Hypertrophy of iris vessels (h) Digest preparations of these abnormal proliferations (i) Histological studies (j) Electron microscopical studies (5) Man. The Premature Infant . 527
Biology of Platelet Purinergic Receptors and Implications for Platelet Heterogeneity

Platelets are small anucleated cells present only in mammals. Platelets mediate intravascular hemostatic balance, prevent interstitial bleeding, and have a major role in thrombosis. Activation of platelet purinergic receptors is instrumental in initiation of hemostasis and formation of the hemostatic plug, although this activation process becomes problematic in pathological settings of thrombosis. This review briefly outlines the roles and function of currently known platelet purinergic receptors (P1 and P2) in the setting of hemostasis and thrombosis. Additionally, we discuss recent novel studies on purinergic receptor distribution according to heterogeneous platelet size, and the possible implication of this distribution on hemostatic function.
Functionalized carbon micro/nanostructures for biomolecular detection

Advancements in the micro-and nano-scale fabrication techniques have opened up new avenues for the development of portable, scalable and easier-to-use biosensors. Over the last few years, electrodes made of carbon have been widely used as sensing units in biosensors due to their attractive physiochemical properties. The aim of this research is to investigate different strategies to develop functionalized high surface carbon micro/nano-structures for electrochemical and biosensing devices. High aspect ratio three-dimensional carbon microarrays were fabricated via carbon microelectromechanical systems (C-MEMS) technique, which is based on pyrolyzing pre-patterned organic photoresist polymers. To further increase the surface area of the carbon microstructures, surface porosity was introduced by two strategies, i.e. (i) using F127 as porogen and (ii) oxygen reactive ion etch (RIE) treatment. Electrochemical characterization showed that porous carbon thin film electrodes prepared by using F127 as porogen had an effective surface area (Aeff 185%) compared to the conventional carbon electrode. To achieve enhanced electrochemical sensitivity for C-MEMS based functional devices, graphene was conformally coated onto high aspect ratio three-dimensional (3D) carbon micropillar arrays using electrostatic spray deposition (ESD) technique. The amperometric response of graphene/carbon micropillar electrode arrays exhibited higher electrochemical activity, improved charge transfer and a linear response towards H2O2 detection between 250μM to 5.5mM. Furthermore, carbon structures with dimensions from 50 nano-to micrometer level have been fabricated by pyrolyzing photo-nanoimprint lithography patterned organic resist polymer. Microstructure, elemental composition and resistivity characterization of the carbon nanostructures produced by this process were very similar to conventional photoresist derived carbon. Surface functionalization of the carbon nanostructures was performed using direct amination technique. Considering the need for requisite functional groups to covalently attach bioreceptors on the carbon surface for biomolecule detection, different oxidation techniques were compared to study the types of carbon–oxygen groups formed on the surface and their percentages with respect to different oxidation pretreatment times. Finally, a label-free detection strategy using signaling aptamer/protein binding complex for platelet-derived growth factor oncoprotein detection on functionalized three-dimensional carbon microarrays platform was demonstrated. The sensor showed near linear relationship between the relative fluorescence difference and protein concentration even in the sub-nanomolar range with an excellent detection limit of 5 pmol.
Implementation of Adaptive Neuro Fuzzy Inference System for Malaria Diagnosis (Case Study: Kwesimintsim Polyclinic)

Health issues have become one of the problems bedeviling most developing and under-developed countries in our world today. Ghana is of no exception from this menace especially in Africa. One of the prevalent diseases battling with Ghanaians and Africa as a whole is the malaria disease. In 1994, the WHO reported that malaria and measles were the most common causes of premature death. in children under five(5) years. Diagnosis of malaria in many cases has not been accurate by most doctors or physicians due to external human factors such as fatigue and hastiness among others, thereby leading to patients being subjected to treatment again which also come with cost. This paper employs the use of Adaptive Neuro-Fuzzy Inference System (ANFIS) to provide a better option for malaria diagnosis than the traditional diagnosis method which is characterized by erotic guess work and observation of patients by doctors. Datasets of patients divided into training and checking data were used to train the ANFIS. The results tested after training showed that ANFIS has the ability to diagnose malaria efficiently than the traditional method with very minimal error.
Shear Strengthening of a PC Bridge Girder with NSM CFRP Rectangular Bars

Bridges worldwide are falling into a state of disrepair caused by deterioration, traffic overloading, and poor maintenance. It is estimated that over 100,000 of the half million existing bridges in the US are in need of repair or replacement. Although the full replacement option could be viable, it is an expensive solution with significant disruption of service. This paper focuses on the use of carbon fiber reinforced polymer (CFRP) rectangular bars installed as near surface mounted (NSM) reinforcement for shear strengthening in conjunction with an externally bonded pre-cured CFRP laminate to increase the flexural capacity of a prestressed concrete (PC) bridge girder. The specimen, which was removed from an overloaded bridge in Kansas was strengthened and tested in the laboratory. Test results showed that the proposed NSM reinforcement technique represents an effective solution to increase shear capacity.
Rateless Codes Design Scheme Based on Two Stages

Current rateless codes coding schemes ignored the order recovery of packets. To cope with this problem, average delay and maximum memory consumption were proposed as performance indices to characterize the order recovery performance, then a coding scheme based on two stages coding was proposed to improve the order recovery performance. Encoding of the front k coded symbols is the first stage, which the i th coded symbol is compose of the i th packet and other d i -1 packets which are chosen from the front i-1 packets with equal probability. Encoding of the remaining infinite coded symbols is the second stage which the packets are chosen from all packets equal probably. The simulation results show that the rateless codes from the proposed scheme have better order recovery performance, meanwhile have high bandwidth efficiency and good uniformity recovery than LT codes.
Endothelial K+ channel lacks the Ca2+ sensitivity‐regulating β subunit

Hyperpolarizing large‐conductance, Ca2+‐activated K+ channels (BK) are important modulators of vascular smooth muscle and endothelial cell function. In vascular smooth muscle cells. BK are composed of pore‐forming α subunits and modulatory β subunits. However. expression. composition. and function of BK subunits in endothelium have not been studied so far. In patch‐clamp experiments we identified BK (283 pS) in intact endothe‐lium of porcine aortic tissue slices. The BK opener DHS‐I (0.05–0.3 μmol/l). stimulating BK activity only in the presence of β subunits. had no effect on BK in endothelium whereas the α subunit selective BK opener NS1619 (20 μmol/l) markedly increased channel activity. Correspondingly. mRNA expression of the β subunit was undetectable in endothelium. whereas α subunit expression was demonstrated. To investigate the functional role of β subunits. we transfected the β subunit into a human endothelial cell line (EA.hy 926). β subunit expression resulted in an increased Ca2+ sensitivity of BK activity: the potential of half‐maximal activation (Vw2) shifted from 73.4 mV to 49.6 mV at 1 μmol/l [Ca2+]i and an decrease of the EC50 value for [Ca2+]i by 1 μMat + 60 mV was observed. This study demonstrates that BK channels in endothelium are composed of α subunits without association to β subunits. The lack of the β subunit indicates a substantially different channel regulation in endothelial cells compared to vascular smooth muscle cells. —Papassotiriou. J. Kohler. R. Prenen. J. Krause. H. Akbar. M. Egger‐mont. J. Paul. M. Distler. A. Nilius. B. Hoyer. J. Endothelial K+ channel lacks the Ca2+ sensitivity‐regulating β subunit. FASEBJ. 14. 885–894 (2000)
Common cuckoos (Cuculus canorus) affect the bacterial diversity of the eggshells of their great reed warbler (Acrocephalus arundinaceus) hosts

The common cuckoo (Cuculus canorus) is an avian brood parasite, laying its eggs in the nests of other bird species, where these hosts incubate the parasitic eggs, feed and rear the nestlings. The appearance of a cuckoo egg in a host nest may change the bacterial community in the nest. This may have consequences on the hatchability of host eggs, even when hosts reject the parasitic egg, typically within six days after parasitism. The present study revealed the bacterial community of cuckoo eggshells and those of the great reed warbler (Acrocephalus arundinaceus), one of the main hosts of cuckoos. We compared host eggs from non-parasitized clutches, as well as host and cuckoo eggs from parasitized clutches. As incubation may change bacterial assemblages on eggshells, we compared these egg types in two stages: the egg-laying stage, when incubation has not been started, and the mid-incubation stage (ca. on days 5–7 in incubation), where heat from the incubating female dries eggshells. Our results obtained by the 16S rRNA gene sequencing technique showed that fresh host and cuckoo eggs had partially different bacterial communities, but they became more similar during incubation in parasitized nests. Cluster analysis revealed that fresh cuckoo eggs and incubated host eggs in unparasitized nests (where no cuckoo effect could have happened) were the most dissimilar from the other groups of eggs. Cuckoo eggs did not reduce the hatchability of great reed warbler eggs. Our results on the cuckoo-great reed warbler relationship supported the idea that brood parasites may change bacterial microbiota in the host nest. Further studies should reveal how bacterial communities of cuckoo eggshells may vary by host-specific races (gentes) of cuckoos.
Context-Aware Patch Generation for Better Automated Program Repair

The effectiveness of search-based automated program repair is limited in the number of correct patches that can be successfully generated. There are two causes of such limitation. First, the search space does not contain the correct patch. Second, the search space is huge and therefore the correct patch cannot be generated (ie correct patches are either generated after incorrect plausible ones or not generated within the time budget). To increase the likelihood of including the correct patches in the search space, we propose to work at a fine granularity in terms of AST nodes. This, however, will further enlarge the search space, increasing the challenge to find the correct patches. We address the challenge by devising a strategy to prioritize the candidate patches based on their likelihood of being correct. Specifically, we study the use of AST nodes' context information to estimate the likelihood. In this paper, we propose CapGen, a context-aware patch generation technique. The novelty which allows CapGen to produce more correct patches lies in three aspects: (1) The fine-granularity design enables it to find more correct fixing ingredients; (2) The context-aware prioritization of mutation operators enables it to constrain the search space; (3) Three context-aware models enable it to rank correct patches at high positions before incorrect plausible ones. We evaluate CapGen on Defects4J and compare it with the state-of-the-art program repair techniques. Our evaluation shows that CapGen outperforms and complements existing techniques. CapGen achieves a high precision of 84.00% and can prioritize the correct patches before 98.78% of the incorrect plausible ones.
Optimal DNN primitive selection with partitioned boolean quadratic programming

Deep Neural Networks (DNNs) require very large amounts of computation, and many different algorithms have been proposed to implement their most expensive layers, each of which has a large number of variants with different trade-offs of parallelism, locality, memory footprint, and execution time. In addition, specific algorithms operate much more efficiently on specialized data layouts. We state the problem of optimal primitive selection in the presence of data layout transformations, and show that it is NP-hard by demonstrating an embedding in the Partitioned Boolean Quadratic Assignment problem (PBQP). We propose an analytic solution via a PBQP solver, and evaluate our approach experimentally by optimizing several popular DNNs using a library of more than 70 DNN primitives, on an embedded platform and a general purpose platform. We show experimentally that significant gains are possible versus the state of the art vendor libraries by using a principled analytic solution to the problem of primitive selection in the presence of data layout transformations.
Control of Mucosal Candidiasis in the Zebrafish Swim Bladder Depends on Neutrophils That Block Filament Invasion and Drive Extracellular-Trap Production

ABSTRACT Candida albicans is a ubiquitous mucosal commensal that is normally prevented from causing acute or chronic invasive disease. Neutrophils contribute to protection in oral infection but exacerbate vulvovaginal candidiasis. To dissect the role of neutrophils during mucosal candidiasis, we took advantage of a new, transparent zebrafish swim bladder infection model. Intravital microscopic tracking of individual animals revealed that the blocking of neutrophil recruitment leads to rapid mortality in this model through faster disease progression. Conversely, artificial recruitment of neutrophils during early infection reduces disease pressure. Noninvasive longitudinal tracking showed that mortality is a consequence of C. albicans breaching the epithelial barrier and invading surrounding tissues. Accordingly, we found that a hyperfilamentous C. albicans strain breaches the epithelial barrier more frequently and causes mortality in immunocompetent zebrafish. A lack of neutrophils at the infection site is associated with less fungus-associated extracellular DNA and less damage to fungal filaments, suggesting that neutrophil extracellular traps help to protect the epithelial barrier from C. albicans breach. We propose a homeostatic model where C. albicans disease pressure is balanced by neutrophil-mediated damage of fungi, maintaining this organism as a commensal while minimizing the risk of damage to host tissue. The unequaled ability to dissect infection dynamics at a high spatiotemporal resolution makes this zebrafish model a unique tool for understanding mucosal host-pathogen interactions.