Miracle-dz/UniFAR-FTUs huggingface dataset:
Pertinent Shape Effects of Gold Nanospheres and Nanostellates

Modulating optical resonances in plasmonic resonators were easily achieved by virtue of their constituent composition, size as well as shape. Such confinement of electric field in the nano-regime enhances extra-ordinarily the light-matter interaction, further enabling wide range of applications in nanophotonics, SERS etc. Herein, we compare and contrast the surface plasmon modes of Au nanospheres and nanostellates, the visibly distinct morphologies of which not only correlates exceptionally well with their structure-property functional relationships, but also articulate their respective growth mechanisms in a rather meticulous manner. Higher amplification of analyte Raman signals visibly demonstrates the increased number of hot-spots with reference to their surface morphology and roughness.
Expression of the Xylulose 5-Phosphate Phosphoketolase Gene, xpkA, from Lactobacillus pentosus MD363 Is Induced by Sugars That Are Fermented via the Phosphoketolase Pathway and Is Repressed by Glucose Mediated by CcpA and the Mannose Phosphoenolpyruvate Phosphotransferase System

ABSTRACT Purification of xylulose 5-phosphate phosphoketolase (XpkA), the central enzyme of the phosphoketolase pathway (PKP) in lactic acid bacteria, and cloning and sequence analysis of the encoding gene, xpkA, from Lactobacillus pentosus MD363 are described. xpkA encodes a 788-amino-acid protein with a calculated mass of 88,705 Da. Expression of xpkA in Escherichia coli led to an increase in XpkA activity, while an xpkA knockout mutant of L. pentosus lost XpkA activity and was not able to grow on energy sources that are fermented via the PKP, indicating that xpkA encodes an enzyme with phosphoketolase activity. A database search revealed that there are high levels of similarity between XpkA and a phosphoketolase from Bifidobacterium lactis and between XpkA and a (putative) protein present in a number of evolutionarily distantly related organisms (up to 54% identical residues). Expression of xpkA in L. pentosus was induced by sugars that are fermented via the PKP and was repressed by glucose mediated by carbon catabolite protein A (CcpA) and by the mannose phosphoenolpyruvate phosphotransferase system. Most of the residues involved in correct binding of the cofactor thiamine pyrophosphate (TPP) that are conserved in transketolase, pyruvate decarboxylase, and pyruvate oxidase were also conserved at a similar position in XpkA, implying that there is a similar TPP-binding fold in XpkA.
Controller Area Network (CAN) Schedulability Analysis with FIFO Queues

Controller Area Network (CAN) is widely used in automotive applications. Existing schedulability analysis for CAN is based on the assumption that the highest priority message ready for transmission at each node on the network will be entered into arbitration on the bus. However, in practice, some CAN device drivers implement FIFO rather than priority-based queues invalidating this assumption. In this paper, we introduce response time analysis and optimal priority assignment policies for CAN messages in networks where some nodes use FIFO queues while other nodes use priority queues. We show, via a case study and experimental evaluation, the detrimental impact that FIFO queues have on the real-time performance of CAN.
Self-Stabilizing Diffusion

This paper deals with a peculiar instance of the consensus problem. In our scenario, the system can be assimilated to an irregular network composed of clusters of processing units. Each unit holds a ”copy” of a value, that changes continuously according with a known function. The basic problem we address is to keep all the copies sufficiently close to the real value, given that most units cannot keep the local copy of the value exactly updated, with a minimal computational load. With respect to the ”precision” of the local copy of the global value, we distinguish two kinds of units: a restricted number of units that continuously keep the correct value, upon which any other unit should agree, and the rest of the units, that can only estimate locally the current global value. We do not investigate the way in which the former units keep their copies exactly updated: since we count a few units of this kind in the system, they may use an expensive strategy. On the contrary, we are interested in the behavior of the rest of the system. The precision of the local estimate of the other units progressively degrades, and they need to periodically refresh their local estimate in order to keep it acceptably near to the global value. Our problem is the design of a protocol that performs this task. The relevance of the problem should become evident if we recognize that the above description is a paraphrase of the clock synchronization problem: a few units in the system hold accurate (and expensive) clocks, while the others periodically synchronize their in-accurate (and cheap) clocks with the accurate ones. The interested reader can find a technical discussion of the problem and its practical solution in Internet in [7]: the protocol suite is known as Network Time Protocol (NTP).
Mechanisms of bone response to injury

Bone, despite its relatively inert appearance, is a tissue that is capable of adapting to its environment. Wolff’s law, first described in the 19th century, describes the ability of bone to change structure depending on the mechanical forces applied to it. The mechanostat model extended this principle and suggested that the amount of strain a bone detects depends on bone strength and the amount of muscle force applied to the bone. Experimental studies have found that low-magnitude, high-frequency mechanical loading is considered to be the most effective at increasing bone formation. The osteocyte is considered to be the master regulator of the bone response to mechanical loading. Deformation of bone matrix by mechanical loading is thought to result in interstitial fluid flow within the lacunar–canalicular system, which may activate osteocyte mechanosensors, leading to changes in osteocyte gene expression and ultimately increased bone formation and decreased bone resorption. However, repetitive strain applied to bone can result in microcracks, which may propagate and coalesce, and if not repaired predispose to catastrophic fracture. Osteocytes are a key component in this process, whereby apoptotic osteocytes in an area of microdamage promote targeted remodeling of the damaged bone. If fractures do occur, fracture repair can be divided into 2 types: primary and secondary healing. Secondary fracture repair is the most common and is a multistage process consisting of hematoma formation and acute inflammation, callus formation, and finally remodeling, whereby bone may return to its original form.
Analyzing the Robustness of Scheduling Algorithms Using Divisible Load Theory on Heterogeneous Systems

Arbitrarily divisible workloads are present in a large class of scientific applications, such as N-body simulations, Monte Carlo simulations, CFD applications, and others. Divisible load theory (DLT) provides a tractable approach to the scheduling of arbitrarily divisible workloads. High performance parallel and distributed systems may operate in an unreliable environment, and a robust system is expected to deliver a certain level of performance when operating in such an environment. To the best of our knowledge, this is the first work to study and analyze the robustness of DLT algorithms. Using simulations, a study of the resiliency of DLT to variations in certain system features, such as the network latency, the network bandwidth, and the processor availability on a single level tree topology is presented. The simulation results demonstrate the robustness of the DLT algorithms under certain application and system characteristics.
Detection of human papillomavirus DNA in cytologically normal women and subsequent cervical squamous intraepithelial lesions.

BACKGROUND Human papillomavirus (HPV) infection has been strongly associated with cervical carcinoma and its cytologic precursors, squamous intraepithelial lesions (SIL). We investigated the risk of SIL prospectively following polymerase chain reaction (PCR)-based DNA testing for a wide range of genital HPV types in a cohort of initially cytologically normal women, to clarify the role of HPV in the etiology of SIL. METHODS Starting in April 1989, 17,654 women who were receiving routine cytologic screening at Kaiser Permanente (Portland, OR) were followed for the development of incident SIL. During follow-up, 380 incident case patients and 1037 matched control subjects were eligible for this nested case-control study. Cervical lavages collected at enrollment and, later, at the time of case diagnosis (or the corresponding time for selection of control subjects) were tested for HPV DNA using a PCR-based method. The data were analyzed as contingency tables with two-sided P values or, for multivariable analyses, using odds ratios (ORs) with 95% confidence intervals (CIs). RESULTS In comparison with initially HPV-negative women, women who tested positive for HPV DNA at enrollment were 3.8 times (95% CI = 2.6-5.5) more likely to have low-grade SIL subsequently diagnosed for the first time during follow-up and 12.7 times more likely (95% CI = 6.2-25.9) to develop high-grade SIL. At the time of diagnosis, the cross-sectional association of HPV DNA and SIL was extremely strong (OR = 44.4 and 95% CI = 24.2-81.5 for low-grade SIL and OR = 67.1 and 95% CI = 19.3-233.7 for high-grade SIL). HPV16 was the virus type most predictive of SIL, even low-grade SIL. CONCLUSIONS These findings are consistent with the hypothesis that HPV infection is the primary cause of cervical neoplasia. Furthermore, they support HPV vaccine research to prevent cervical cancer and efforts to develop HPV DNA diagnostic tests.
Towards a global schema for web entities

Popular entities often have thousands of instances on the Web. In this paper, we focus on the case where they are presented in table-like format, namely appearing with their attribute names. It is observed that, on one hand, for the same entity, different web pages often incorporate different attributes; on the other, for the same attribute, different web pages often use different attribute names (labels). Therefore, it is imaginably difficult to produce a global attribute schema for all the web entities of a given entity type based on their web instances, although the global attribute schema is usually highly desired in web entity instances integration and web object extraction. To this end, we propose a novel framework of automatically learning a global attribute schema for all web entities of one specific entity type. Under this framework, an iterative instances extraction procedure is first employed to extract sufficient web entity instances to discover enough attribute labels. Next, based on the labels, entity instances, and related web pages, a maximum entropy-based schema discovery approach is adopted to learn the global attribute schema for the target entity type. Experimental results on the Chinese Web achieve weighted average Fscores of 0.7122 and 0.7123 on two global attribute schemas for person-type and movie-type web entities, respectively. These results show that our framework is general, efficient and effective.
Dynamic CT Perfusion Imaging for the Detection of Crossed Cerebellar Diaschisis in Acute Ischemic Stroke

Objective Although the detection of crossed cerebellar diaschisis (CCD) by means of different imaging modalities is well described, little is known about its diagnosis by computed tomography perfusion (CTP) imaging. We investigated the detection rate of CCD by CTP imaging and the factors related to CCD on CTP images in patients with acute ischemic stroke. Materials and Methods CT perfusion maps of cerebral blood volume (CBV), cerebral blood flow (CBF), mean transit time (MTT), and time-to-peak (TTP) obtained from 81 consecutive patients affected by an acute ischemic stroke were retrospectively reviewed. Whole-brain perfusion maps were obtained with a multichannel CT scanner using the toggling-table technique. The criteria for CCD was a unilateral supratentorial ischemic lesion and an accompanying decrease in perfusion of the contralateral cerebellar hemisphere on the basis of CTP maps by visual inspection without a set threshold. Maps were quantitatively analyzed in CCD positive cases. Results The criteria for CCD were fulfilled in 25 of the 81 cases (31%). Detection rates per CTP map were as follows: MTT (31%) > TTP (21%) > CBF (9%) > CBV (6%). Supratentorial ischemic volume, degree of perfusion reduction, and infratentorial asymmetry index correlated strongly (R, 0.555-0.870) and significantly (p < 0.05) with each other in CCD-positive cases. Conclusion It is possible to detect CCD on all four of the CTP-based maps. Of these maps, MTT is most sensitive in detecting CCD. Our data indicate that CTP imaging is a valid tool for the diagnosis of CCD in patients affected by an acute hemispheric stroke.
Distribution of neuropetide Y‐like immunoreactivity in the hypothalamus of the adult golden hamster

The distribution of neuropeptide Y (NPY)‐like immunoreactivity within the hypothalamus of the adult golden hamster was investigated with conventional immunohistochemical techniques. Neuropeptide Y immunoreactive cell bodies were found in greatest numbers in the arcuate nucleus while a few stained perikarya were seen in the internal and subependymal zones of the median eminence. Isolated perikarya were observed in the anterior commissure and supracommissural portion of the interstitial nucleus of the stria terminalis. Immunoreactive axons were located throughout the hypothalamus with the highest concentrations in the subependymal and internal zones of the median eminence, the interstitial nucleus of the stria terminalis, the medial preoptic area, and in the following nuclei: periventricular, suprachiasmatic, paraventricular, perifornical, median preoptic, and arcuate. Moderate to dense plexuses of immunoreactive fibers were observed in the anterior, lateral, and posterior hypothalamic areas and in the infundibular stalk. The supraoptic nucleus and lateral preoptic area displayed a small number of labeled axons whereas the ventromedial nucleus contained only a few fibers. NPY immunoreactive fibers were present in the optic tract and in the dorsomedial aspect of the optic chiasm. Labeled fibers penetrated the ependymal lining of the third ventricle throughout the ventral aspect of the periventricular zone. Additional fibers were observed in the pia lining the ventral aspect of the hypothalamus. This systematic analysis of hypothalamic NPY immunoreactivity in the adult golden hamster suggests that a portion of the labeled fibers display a distribution that is similar to previously described noradrenergic fibers in the hypothalamus.
Memory, attention, and executive function in chronic fatigue syndrome.

OBJECTIVES--To examine cognitive function in chronic fatigue syndrome. METHODS--Twenty patients with chronic fatigue syndrome recruited from primary care and 20 matched normal controls were given CANTAB computerised tests of visuospatial memory, attention, and executive function, and verbal tests of letter and category fluency and word association learning. RESULTS: Patients with chronic fatigue syndrome were impaired, predominantly in the domain of memory but their pattern of performance was unlike that of patients with amnesic syndrome or dementia. They were normal on tests of spatial pattern recognition memory, simultaneous and delayed matching to sample, and pattern-location association learning. They were impaired on tests of spatial span, spatial working memory, and a selective reminding condition of the pattern-location association learning test. An executive test of planning was normal. In an attentional test, eight subjects with chronic fatigue syndrome were unable to learn a response set; the remainder exhibited no impairment in the executive set shifting phase of the test. Patients with chronic fatigue syndrome were also impaired on verbal tests of unrelated word association learning and letter fluency. CONCLUSION--Patients with chronic fatigue syndrome have reduced attentional capacity resulting in impaired performance on effortful tasks requiring planned or self ordered generation of responses from memory.
Identification of Thyroid Hormone Receptor Binding Sites and Target Genes Using ChIP-on-Chip in Developing Mouse Cerebellum

Thyroid hormone (TH) is critical to normal brain development, but the mechanisms operating in this process are poorly understood. We used chromatin immunoprecipitation to enrich regions of DNA bound to thyroid receptor beta (TRβ) of mouse cerebellum sampled on post natal day 15. Enriched target was hybridized to promoter microarrays (ChIP-on-chip) spanning −8 kb to +2 kb of the transcription start site (TSS) of 5000 genes. We identified 91 genes with TR binding sites. Roughly half of the sites were located in introns, while 30% were located within 1 kb upstream (5′) of the TSS. Of these genes, 83 with known function included genes involved in apoptosis, neurodevelopment, metabolism and signal transduction. Two genes, MBP and CD44, are known to contain TREs, providing validation of the system. This is the first report of TR binding for 81 of these genes. ChIP-on-chip results were confirmed for 10 of the 13 binding fragments using ChIP-PCR. The expression of 4 novel TH target genes was found to be correlated with TH levels in hyper/hypothyroid animals providing further support for TR binding. A TRβ binding site upstream of the coding region of myelin associated glycoprotein was demonstrated to be TH-responsive using a luciferase expression system. Motif searches did not identify any classic binding elements, indicating that not all TR binding sites conform to variations of the classic form. These findings provide mechanistic insight into impaired neurodevelopment resulting from TH deficiency and a rich bioinformatics resource for developing a better understanding of TR binding.
The zen of the web

Michael N. Huhns University of South Carolina The Zen of the Web In contrast to the original Web’s content, which was designed for human use and comprehension, the Semantic Web’s1 content is for computer use and understanding. To date, however, most efforts have focused on the understanding rather than use. This special issue of IC focuses on the use of the Web by computer systems and agents. By supporting the notion of “getting work done,” the Semantic Web will become more useful, valuable, and pragmatic. Many organizations are attempting to make the Web computer-friendly via Web services, but current incarnations of these technologies are subject to several limitations:
Understanding International Migration using Tensor Factorization

Understanding human migration is of great interest to demographers and social scientists. User generated digital data has made it easier to study such patterns at a global scale. Geo coded Twitter data, in particular, has been shown to be a promising source to analyse large scale human migration. But given the scale of these datasets, a lot of manual effort has to be put into processing and getting actionable insights from this data. In this paper, we explore feasibility of using a new tool, tensor decomposition, to understand trends in global human migration. We model human migration as a three mode tensor, consisting of (origin country, destination country, time of migration) and apply CP decomposition to get meaningful low dimensional factors. Our experiments on a large Twitter dataset spanning 5 years and over 100M tweets show that we can extract meaningful migration patterns.
Fidelity Variants of RNA Dependent RNA Polymerases Uncover an Indirect, Mutagenic Activity of Amiloride Compounds

In a screen for RNA mutagen resistance, we isolated a high fidelity RNA dependent RNA polymerase (RdRp) variant of Coxsackie virus B3 (CVB3). Curiously, this variant A372V is also resistant to amiloride. We hypothesize that amiloride has a previously undescribed mutagenic activity. Indeed, amiloride compounds increase the mutation frequencies of CVB3 and poliovirus and high fidelity variants of both viruses are more resistant to this effect. We hypothesize that this mutagenic activity is mediated through alterations in intracellular ions such as Mg2+ and Mn2+, which in turn increase virus mutation frequency by affecting RdRp fidelity. Furthermore, we show that another amiloride-resistant RdRp variant, S299T, is completely resistant to this mutagenic activity and unaffected by changes in ion concentrations. We show that RdRp variants resist the mutagenic activity of amiloride via two different mechanisms: 1) increased fidelity that generates virus populations presenting lower basal mutation frequencies or 2) resisting changes in divalent cation concentrations that affect polymerase fidelity. Our results uncover a new antiviral approach based on mutagenesis.
Revision vs. Update: Taking a Closer Look

Belief revision and belief update are two of the most important types of belief change. Although similar in some ways, these two processes are believed to be fundamentally different. In this paper we take a closer look at belief revision (as formalized by Alchourrón, Gärdenfors and Makinson [1]) and belief update (as modelled by Katsuno and Mendelzon [4]). The results we obtain herein show that the two processes differ, not so much in the way they change a fixed belief state K , but rather on how changes at different theories are related to each other.
Opposite Effects of Early-Life Competition and Developmental Telomere Attrition on Cognitive Biases in Juvenile European Starlings

Moods are enduring affective states that we hypothesise should be affected by an individual’s developmental experience and its current somatic state. We tested whether early-life adversity, induced by manipulating brood size, subsequently altered juvenile European starlings’ (Sturnus vulgaris) decisions in a judgment bias task designed to provide a cognitive measure of mood. We predicted that starlings from larger broods, specifically those that had experienced more nest competitors larger than themselves would exhibit reduced expectation of reward, indicative of a ‘pessimistic’, depression-like mood. We used a go/no-go task, in which 30 starlings were trained to probe a grey card disc associated with a palatable mealworm hidden underneath and avoid a different shade of grey card disc associated with a noxious quinine-injected mealworm hidden underneath. Birds’ response latencies to the trained stimuli and also to novel, ambiguous stimuli intermediate between these were subsequently tested. Birds that had experienced greater competition in the nest were faster to probe trained stimuli, and it was therefore necessary to control statistically for this difference in subsequent analyses of the birds’ responses to the ambiguous stimuli. As predicted, birds with more, larger nest competitors showed relatively longer latencies to probe ambiguous stimuli, suggesting reduced expectation of reward and a ‘pessimistic’, depression-like mood. However, birds with greater developmental telomere attrition—a measure of cellular aging associated with increased morbidity and reduced life-expectancy that we argue could be used as a measure of somatic state—showed shorter latencies to probe ambiguous stimuli. This would usually be interpreted as evidence for a more positive or ‘optimistic’ affective state. Thus, increased competition in the nest and poor current somatic state appear to have opposite effects on cognitive biases. Our results lead us to question whether increased expectation of reward when presented with ambiguous stimuli always indicates a more positive affective state. We discuss the possibility that birds in poor current somatic state may adopt a ’hungry’ cognitive phenotype that could drive behaviour commonly interpreted as ‘optimism’ in food-rewarded cognitive bias tasks.