Miracle-dz/UniFAR-FTUs huggingface dataset:
Soluble peptide–MHC monomers cause activation of CD8+ T cells through transfer of the peptide to T cell MHC molecules

T cell receptor (TCR)-mediated activation of CD4+ T cells is known to require multivalent engagement of the TCR by, for example, oligomeric peptide–MHC complexes. In contrast, for CD8+ T cells, there is evidence for TCR-mediated activation by univalent engagement of the TCR. We have here compared oligomeric and monomeric Ld and Kb peptide–MHC complexes and free peptide as stimulators of CD8+ T cells expressing the 2C TCR. We found that the monomers are indeed effective in activating naïve and effector CD8+ T cells, but through an unexpected mechanism that involves transfer of peptide from soluble monomers to T cell endogenous MHC (Kb) molecules. The result is that T cells, acting as antigen-presenting cells, are able to activate other naïve T cells.
Draft Genome Sequence of the Phyllosphere Model Bacterium Pantoea agglomerans 299R

ABSTRACT Bacteria belonging to the genus Pantoea are common colonizers of plant leaf surfaces. Here, we present the draft genome sequence of Pantoea agglomerans 299R, a phyllosphere isolate that has become a model strain for studying the ecology of plant leaf-associated bacterial commensals.
Cytochrome bd Oxidase, Oxidative Stress, and Dioxygen Tolerance of the Strictly Anaerobic Bacterium Moorella thermoacetica

ABSTRACT The gram-positive, thermophilic, acetogenic bacterium Moorella thermoacetica can reduce CO2 to acetate via the Wood-Ljungdahl (acetyl coenzyme A synthesis) pathway. This report demonstrates that, despite its classification as a strict anaerobe, M. thermoacetica contains a membrane-bound cytochrome bd oxidase that can catalyze reduction of low levels of dioxygen. Whole-cell suspensions of M. thermoacetica had significant endogenous O2 uptake activity, and this activity was increased in the presence of methanol or CO, which are substrates in the Wood-Ljungdahl pathway. Cyanide and azide strongly (∼70%) inhibited both the endogenous and CO/methanol-dependent O2 uptake. UV-visible light absorption and electron paramagnetic resonance spectra of n-dodecyl-β-maltoside extracts of M. thermoacetica membranes showed the presence of a cytochrome bd oxidase complex containing cytochrome b561, cytochrome b595, and cytochrome d (chlorin). Subunits I and II of the bd oxidase were identified by N-terminal amino acid sequencing. The M. thermoacetica cytochrome bd oxidase exhibited cyanide-sensitive quinol oxidase activity. The M. thermoacetica cytochrome bd (cyd) operon consists of four genes, encoding subunits I and II along with two ABC-type transporter proteins, homologs of which in other bacteria are required for assembly of the bd complex. The level of this cyd operon transcript was significantly increased when M. thermoacetica was grown in the absence of added reducing agent (cysteine + H2S). Expression of a 35-kDa cytosolic protein, identified as a cysteine synthase (CysK), was also induced by the nonreducing growth conditions. The combined evidence indicates that cytochrome bd oxidase and cysteine synthase protect against oxidative stress and contribute to the limited dioxygen tolerance of M. thermoacetica.
Gamma knife surgery for trigeminal neuralgia: outcomes and prognostic factors.

OBJECT Microvascular decompression (MVD) and percutaneous ablation surgery have historically been the treatments of choice for medically refractory trigeminal neuralgia (TN). Gamma knife surgery (GKS) has been used as an alternative, minimally invasive treatment in TN. In the present study, the authors evaluated the long-term results of GKS in the treatment of TN. METHODS From 1996 to 2003, 151 cases of TN were treated with GKS. In this group, radiosurgery was performed once in 136 patients, twice in 14 patients, and three times in one patient. The types of TN were as follows: 122 patients with typical TN, three with atypical TN, four with multiple sclerosis-associated TN, and seven with TN and a history of a cavernous sinus tumor. In each case, the chosen radiosurgical target was located 2 to 4 mm anterior to the entry of the trigeminal nerve into the pons. The maximal radiation doses ranged from 50 to 90 Gy. The median age of the patients was 68 years (range 22-90 years), and the median time from diagnosis to GKS was 72 months (range 1-276 months). The median follow up was 19 months (range 2-96 months). Clinical outcomes and postradiosurgical magnetic resonance (MR) imaging studies were analyzed. Univariate and multivariate analyses were performed to evaluate factors that correlated with a favorable, pain-free outcome. The mean time to relief of pain was 24 days (range 1-180 days). Forty-seven, 45, and 34% of patients were pain free without medication at the 1-, 2-, and 3-year follow ups, respectively. Ninety, 77, and 70% of patients experienced some improvement in pain at the 1-, 2-, and 3-year follow ups, respectively. Thirty-three (27%) of 122 patients with initial improvement subsequently experienced pain recurrence a median of 12 months (range 2-34 months) post-GKS. Among those whose symptoms recurred, 14 patients underwent additional GKS, six MVD, four glycerol injection, and one patient a percutaneous radiofrequency rhizotomy. Twelve patients (9%) suffered the onset of new facial numbness post-GKS. Changes on MR images post-GKS were noted in nine patients (7%). On univariate analysis, right-sided neuralgia (p = 0.0002) and a previous neurectomy (p = 0.04) correlated with a pain-free outcome; on multivariate analysis, both rightsided neuralgia (p = 0.032) and patient age (p = 0.05) were statistically significant. New onset of facial numbness following GKS correlated with undergoing more than one GKS (p = 0.002). CONCLUSIONS At the last follow up, GKS effected pain relief in 44% of patients. Some degree of pain improvement at 3 years post-GKS was noted in 70% of patients with TN. Although less effective than MVD, GKS remains a reasonable treatment option for those unwilling or unable to undergo more invasive surgical approaches and offers a low risk of side effects.
Cell Identity Mediates the Response of Arabidopsis Roots to Abiotic Stress

Little is known about the way developmental cues affect how cells interpret their environment. We characterized the transcriptional response to high salinity of different cell layers and developmental stages of the Arabidopsis root and found that transcriptional responses are highly constrained by developmental parameters. These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell layers, several of which correspond to observable physiological changes. We showed that known stress pathways primarily control semiubiquitous responses and used mutants that disrupt epidermal patterning to reveal cell-layer–specific and inter–cell-layer effects. By performing a similar analysis using iron deprivation, we identified common cell-type–specific stress responses and revealed the crucial role the environment plays in defining the transcriptional outcome of cell-fate decisions.
Assessment of Web‐based education resources informing patients about stroke prevention in atrial fibrillation

The importance of ‘shared decision‐making’ is much emphasized in recent clinical guidelines regarding stroke management in atrial fibrillation (AF), more so following the inclusion of non‐vitamin K oral anticoagulants (NOACs) among the treatment options. It is important that patients are navigated through balanced and unbiased information about the available treatment options, so as to understand the risk and benefits associated with the therapies, and to enable them to accordingly communicate their concerns and views with their clinicians prior to therapy selection. Given the increasing popularity of the Internet as a source of health information, the specific objectives of this study were to identify what aspects of thromboprophylaxis (antithrombotic treatment options) were most commonly described in these resources, both in terms of content, that is to report the information provided (quantitative) and the underlying themes underpinning this content, and in terms of how this information might guide patient preferences (qualitative).
Information and Communication Technologies and the Changing Role of the Teacher

ABSTRACT This paper examines the changing role of the teacher in the use of educational Information and Communication Technologies (ICT). Several key issues are explored, including the effects of ICT on teaching and learning, the changing role of the teacher in constructivist learning environments, and the new skills teachers may be expected to acquire in order to make fruitful use of the new technologies. The author argues that the introduction of ICT into schools is raising fundamental questions about the nature of teaching and learning, and may even be challenging our conception of ‘time and place’. The paper offers evaluation of ICT uses in elementary schools in the USA and primary schools in England. It concludes with descriptions of emerging technologies (including relevant website addresses) and the possible contribution these may make to promoting ‘any time, any place’ learning opportunities for the future
Plasma proteolytic activity following burns.

Because a number of metabolic events which are triggered by proteolysis in the bloodstream are activated following trauma, net proteolytic activity (P.A.) in the plasma of 37 pediatric burned patients was measured. The P.A. assay involved incubating plasma with a radioiodinated protein substrate and counting the isotopic activity of the hydrolyzed fragments in the acid-soluble fraction. In patients, plasma P.A. increased in direct proportion to the extent of burn injury. To examine additional trends in plasma P.A. suggested by the patient P.A. data, we measured plasma P.A. in a burned rat model: circulating P.A. was significantly elevated at 6 hours and until at least 2 weeks postburn; infection with Pseudomonas and use of the proteolytic debriding agent, Travase, each further elevated this activity; the plasma P.A. was not directly derived from the burn site. We postulate that this elevated circulating P.A. triggers some of the pathologic as well as some physiologic sequelae which follow burn trauma.
Waveform Characterization of Atrial Fibrillation Using Phase Information

A novel method for characterization of f-wave morphology in atrial fibrillation (AF) is presented. The method decomposes atrial activity into fundamental and harmonic components, dividing each component into short blocks for which the amplitudes, frequencies, and phases are estimated. The phase delays between the fundamental and each of the harmonics, here referred to as harmonic phase relationships, are used as features of f-wave morphology. The estimated waves are clustered into typical morphologic patterns. The performance of the method is illustrated by simulated signals, ECG signals recorded from 36 patients with organized AF, and an ECG signal recorded during drug loading with flecainide. The results show that the method can distinguish a wide variety of f-wave morphologies, and that typical morphologies can be established for further analysis of AF.
Synchronisation and Timing Groups for GSM Networks

GSM networks are optimised for voice services using compact frequency re-use schemes such as 1/1 with fractional loading. GPRS/EDGE codecs require better quality channels to support higher data throughput, i.e. channels with lower collision rates and better average carrier-to-interference ratio (CII). With the continuing growth of mobile data traffic, networks must improve channel quality in a compact re-use environment. To achieve this, we recommend the introduction of timing synchronisation for base stations (BS) in a GSM/GPRS/EDGE network. Our analysis shows that BS synchronisation leads to a reduction in collision rates that can be exploited for either C/I or capacity improvement. More importantly, we propose timing groups (TG) for a synchronized network. In conjunction with frequency planning, TG offers greater flexibility in network design by providing superior quality channels to a category of users without dividing the available spectrum into carrier groups with different re-use schemes
Institutional conditions for sustainable private sector-led urban development projects: A conceptual model

Across the globe sustainable private sector-led urban development projects (SPUDPs) in the built environment rarely commence as real estate developers face several institutional barriers which limit their capacity to develop economic-viable, social-responsible, environmental-friendly urban places. Hence, SPUDPs are a promising development strategy for cities as the scale of such projects could be an effective means to integrate public planning policies and private development decisions with a broader social impact as opposed to solely developing sustainable buildings. However, it is largely unknown how SPUDPs can be effectuated as insight is lacking into institutional conditions that could incentivise real estate developers to make decisions for sustainable urban development practices. This paper explores the institutional conditions, in particular the policy instruments from local planning authorities, that nudge private decision-making to realise SPUDPs, by means of a literature review resulting in a conceptual model. The paper reveals that developers can be incentivised by pro-active local planning bodies using a combination of planning policy instruments which foster a sustainability-sensitive market decision-making environment.
Adhesion and water lubrication of silastic micro-fiber arrays with monolayer surface modification

This study describes different surface energy monolayer modified Silastic micro-fiber Arrays (PDMS Arrays) to enhance the adhesion and water lubrication performances of PDMS Arrays. A multistep fabrication process consisting of electrochemical etching silicon wafers, cast PDMS Arrays, grafts poly(methylhydrosiloxane) (PMHS) onto PDMS Arrays, and modified the PDMS Arrays surface with Poly(ethylene glycol) methyl ether methacrylate(PEG-MA) and Poly(tetrafluoroethylene acrylate) (PTFE-PA), an intrinsically adhesive synthetic polymer. Attenuated total reflectance-fourier transform infrared (ATR-FTIR) spectroscopy was used to monitor the entire process. Results showed that Si-H peak disappeared and two characteristic peaks appeared means PEG-MA and PTFE-PA successful graft to PDMS Arrays Surface. Results from cohesive tests showed that the adhesion of PEG-MA-g-PDMS Arrays enhance, but the adhesion of PTFE-PA-g-PDMS Arrays decrease. Results from water lubrication tests showed that the hydrophilicity of PEG-MA-g-PDMS Arrays increase, contact angle from 122.5° to 94.2°, but PTFE-PA-g-PDMS Arrays contact angle is increased to 129.1°.
Impact of instruction cache replacement policy on the tightness of WCET estimation

Cache memories have been introduced to decrease the access time to the information due to the increasing gap between fast micro-processors and relatively slower main memories. Thus, there is a need for considering caches when validating the temporal behavior of real-time systems, in particular when estimating tasks’ worst-case execution times (WCETs). In this paper, we use new theoretical results to improve a static instruction cache analysis method for set-associative instruction caches with a Pseudo-LRU and a random replacement policies. The proposed method is experimented on three medium-size benchmarks to quantify the impact of the replacement policy on the tightness of WCET estimation.
Investigating the potential of Nigella sativa and thymoquinone in salvaging the embryo from effects of toxic paternal exposure to cyclophosphamide

Background: Exposure to cyclophosphamide (CPA) for cancer treatment results in over-production of reactive oxygen species causes oxidative stress thus affecting the DNA in male germ cell inducing sperm defects. Our goal is to assess the potential effects of Nigella sativa extract (NSE) and thymoquinone (TQ) on sperm and embryo quality following fertlization of sperm produced from germ cells which have been exposed to the damaging alkylating effects of CPA. Methods: Thirty male ICR mice were divided into six groups; (I) Vehicle-treated control (normal saline), (II) CPA-only, (III) TQ-only, (IV) NSE-only, (V) CPA followed by TQ and (VI) CPA followed by NSE. Treatment with 200mg/kg CPA and 10mg/kg of both NSE and TQ were given by intraperitoneal injection. Animals were sacrificed at 33 days by cervical dislocation and sperm from caudal epidydymis were taken for analysis and in vitro fertilization (IVF) with eggs from untreated female. Fertilization rates and embryo development were monitored for 5 days. The result were analysed by using SPSS 16.Results: TQ and NSE supplementation to CPA-exposed male mice have no significant effect (p>0.05) on the total number of sperm if compared to CPA-only exposed mice. NSE and TQ supplementation have been shown to have significant effect (p<0.05) on the percentage of motile sperm as well as the number of abnormal sperm. Four types of abnormalities of the sperm were found which includes folded sperm, amorphous, banana-like and the head lacking of the usual hook. Finally, the embryo quality shows a significant improvement by the supplementation of TQ and NSE to CPA-exposed male mice (p<0.05). Conclusion: Overall, both NSE and TQ have indicated chemopreventive potential against the cytotoxicity of cyclophosphamide on the reproductive capacity and fertility.
Chromium(III) Complexes of D‐Glucosaminic Acid and their Effect on Decreasing Blood Sugar in Vivo

Two chromium(III) complexes of glucosaminic acid were synthesized by neutralization and exchange reaction. The formation of 1 : 1 and 2 : 3 (Cr : glucosaminate) complexes was confirmed by elemental analyses and spectroscopic studies. The effect of the complexes on decreasing blood sugar was investigated on type‐2 diabetes model rats induced by tetraoxypyrimidine. The results indicated that the effect on decreasing blood sugar was comparable to that of picolinate chromium complex (Cr(pic)3) currently used world wide.
Establishment of H2O2‐Induced Premature Senescence in Human Fibroblasts Concomitant with Increased Cellular Production of H2O2

Abstract: Premature senescence of human fibroblasts is established after exposure to an acute sublethal concentration of H2O2. Overexpression of transforming growth factor‐β1 (TGF‐β1) was shown to be responsible for the appearance of the biomarkers of senescence in these conditions. Other studies have shown that incubation of human fibroblasts with TGF‐β1 leads to overexpression of H2O2. In this work, we show an increased production of H2O2 by human fibroblasts as premature senescence is established after an initial exposure to H2O2.
ReRAM-based synaptic device for neuromorphic computing

To compete with nonvolatile FLASH memory technology, we need to develop stackable, cross-point ReRAM device. Although various materials have been reported, it is difficult to meet device criteria such as high speed operation, low power switching, switching uniformity, endurance, long-term retention and selection device for cross-point array. We have investigated various ReRAM devices to meet the nonvolatile memory requirements. We developed wafer scale PCMO-ReRAM devices which exhibit excellent switching uniformity and analog memory behavior. Using PCMO-ReRAM, we can implement analog artificial synapse characteristics for neuromorphic systems. We demonstrated the optimum ReRAM synapse characteristics which are suitable for the neuromorphic application. We compared the time series prediction and face recognition function with varying potentiation and depression characteristics of ReRAM synapse.
Next-generation sequencing reveals somatic mutations that confer exceptional response to everolimus

Background Given the modest responses to everolimus, a mTOR inhibitor, in multiple tumor types, there is a pressing need to identify predictive biomarkers for this drug. Using targeted ultra-deep sequencing, we aimed to explore genomic alterations that confer extreme sensitivity to everolimus. Results We collected formalin-fixed paraffin-embedded tumor/normal pairs from 39 patients (22 with exceptional clinical benefit, 17 with no clinical benefit) who were treated with everolimus across various tumor types (13 gastric cancers, 15 renal cell carcinomas, 2 thyroid cancers, 2 head and neck cancer, and 7 sarcomas). Ion AmpliSeqTM Comprehensive Cancer Panel was used to identify alterations across all exons of 409 target genes. Tumors were sequenced to a median coverage of 552x. Cancer genomes are characterized by 219 somatic single-nucleotide variants (181 missense, 9 nonsense, 7 splice-site) and 22 frameshift insertions/deletions, with a median of 2.1 mutations per Mb (0 to 12.4 mutations per Mb). Overall, genomic alterations with activating effect on mTOR signaling were identified in 10 of 22 (45%) patients with clinical benefit and these include MTOR, TSC1, TSC2, NF1, PIK3CA and PIK3CG mutations. Recurrently mutated genes in chromatin remodeling genes (BAP1; n = 2, 12%) and receptor tyrosine kinase signaling (FGFR4; n = 2, 12%) were noted only in patients without clinical benefit. Conclusions Regardless of different cancer types, mTOR-pathway-activating mutations confer sensitivity to everolimus. Targeted sequencing of mTOR pathway genes facilitates identification of potential candidates for mTOR inhibitors.
The structural correlates of functional deficits in early huntington's disease

Neuropathological studies in Huntington disease (HD) have demonstrated neuronal loss in the striatum, as well as in other brain regions including the cortex. With diffusion tensor MRI we evaluated the hypothesis that the clinical dysfunction in HD is related to regionally specific lesions of circuit‐specific cortico–basal ganglia networks rather than to the striatum only. We included 27 HD and 24 controls from the TRACK‐HD Paris cohort. The following assessments were used: self‐paced tapping tasks, trail B making test (TMT), University of Pennsylvania smell identification test (UPSIT), and apathy scores from the problem behaviors assessment. Group comparisons of fractional anisotropy and mean diffusivity and correlations were performed using voxel‐based analysis. In the cortex, HD patients showed significant correlations between: (i) self paced tapping and mean diffusivity in the parietal lobe at 1.8 Hz and prefrontal areas at 3 Hz, (ii) UPSIT and mean diffusivity in the parietal, and median temporal lobes, the cingulum and the insula, and fractional anisotropy in the insula and the external capsule, (iii) TMT B and mean diffusivity in the white matter of the superior frontal, orbital, temporal, superior parietal and post central areas, and (iv) apathy and fractional anisotropy in the white matter of the rectus gyrus. In the basal ganglia, we found correlations between the self paced tapping, UPSIT, TMT tests, and mean diffusivity in the anterior part of the putamen and the caudate nucleus. In conclusion, disruption of motor, associative and limbic cortico‐striatal circuits differentially contribute to the clinical signs of the disease. Hum Brain Mapp 34:2141–2153, 2013. © 2012 Wiley Periodicals, Inc.