Miracle-dz/UniFAR-FTUs huggingface dataset:
High-throughput, Highly Sensitive Analyses of Bacterial Morphogenesis Using Ultra Performance Liquid Chromatography*

Background: HPLC enables quantification of bacterial cell-wall composition, yet systematic studies across strains, species, and chemical perturbations are lacking. Results: UPLC coupled to computational modeling enables submicroliter injection volumes, and was applied to systematic analysis of several Gram-negative species. Conclusion: Composition is largely decoupled from morphology, although large interspecies differences were evident. Significance: UPLC and automated analysis accelerate discovery regarding peptidoglycan and physiology. The bacterial cell wall is a network of glycan strands cross-linked by short peptides (peptidoglycan); it is responsible for the mechanical integrity of the cell and shape determination. Liquid chromatography can be used to measure the abundance of the muropeptide subunits composing the cell wall. Characteristics such as the degree of cross-linking and average glycan strand length are known to vary across species. However, a systematic comparison among strains of a given species has yet to be undertaken, making it difficult to assess the origins of variability in peptidoglycan composition. We present a protocol for muropeptide analysis using ultra performance liquid chromatography (UPLC) and demonstrate that UPLC achieves resolution comparable with that of HPLC while requiring orders of magnitude less injection volume and a fraction of the elution time. We also developed a software platform to automate the identification and quantification of chromatographic peaks, which we demonstrate has improved accuracy relative to other software. This combined experimental and computational methodology revealed that peptidoglycan composition was approximately maintained across strains from three Gram-negative species despite taxonomical and morphological differences. Peptidoglycan composition and density were maintained after we systematically altered cell size in Escherichia coli using the antibiotic A22, indicating that cell shape is largely decoupled from the biochemistry of peptidoglycan synthesis. High-throughput, sensitive UPLC combined with our automated software for chromatographic analysis will accelerate the discovery of peptidoglycan composition and the molecular mechanisms of cell wall structure determination.
Prethermalization revealed by the relaxation dynamics of full distribution functions

We detail the experimental observation of the non-equilibrium many-body phenomenon prethermalization. We study the dynamics of a rapidly and coherently split one-dimensional Bose gas. An analysis based on the use of full quantum mechanical probability distributions of matter wave interference contrast reveals that the system evolves toward a quasi-steady state. This state, which can be characterized by an effective temperature, is not the final thermal equilibrium state. We compare the evolution of the system to an integrable Tomonaga–Luttinger liquid model, and show that the system dephases to a prethermalized state rather than undergoing thermalization toward a final thermal equilibrium state.
Anaerobic Growth and Fermentation Characteristics of Paecilomyces lilacinus Isolated from Mullet Gut

The anaerobic growth and fermentation of a marine isolate of Paecilomyces lilacinus is described. The fungus was isolated from mullet gut and grew optimally at 30°C and at a salinity of ≥10%. The best growth was obtained with glucose or laminarin as substrate, and the growth yield was 5.0 g (dry weight of fungus) per mol of hexose fermented. Moles of products as a percentage of moles of hexose fermented were acetate, 29.0%; ethanol, 156.6%; CO2, 108.0%; and lactate, 4.3%. Together these products accounted for >80% of hexose carbon. Hydrogen and formate were not detectable as fermentation end products (<0.5%). Other substrates utilized for growth, although less effectively than laminarin or glucose, included the monosaccharides galactose, fructose, arabinose, and xylose and the disaccharides maltose and cellobiose. No growth of the fungus occurred on cellulose, and of a variety of other polysaccharides tested only xylan supported growth.
Design, modeling and implementation of Bi-directional buck and boost converter

This paper presents design, modeling and simulation of an analog controlled bi-directional buck and boost converter. Due importance is given in the model to the effect of non-linear parameters in voltage converters, such as equivalent series resistance ESL of the inductor, ESR of capacitor and RDS(on) of MOSFET switches. Analog controllers are designed using type I, II or III compensation. Simulations of a bi-directional buck and boost converter are performed with Matlab/Simulink. Implementation of the converter with the analog controller is also presented.
Natural HLA-B*2705 Protein Ligands with Glutamine as Anchor Motif

Background: HLA-B27 is strongly associated with ankylosing spondylitis (AS). Results: A change in the position (P) 2 anchor motif was detected in the 3% of HLA-B27 ligands identified, which showed significant homology to pathogenic bacterial sequences. Conclusion: Unusual HLA-B*2705 ligands bind with different conformations to both AS-associated and non-AS-associated HLA-B27 subtypes. Significance: This could be sufficient to initiate autoimmune damage in patients with AS-associated subtypes. The presentation of short viral peptide antigens by human leukocyte antigen (HLA) class I molecules on cell surfaces is a key step in the activation of cytotoxic T lymphocytes, which mediate the killing of pathogen-infected cells or initiate autoimmune tissue damage. HLA-B27 is a well known class I molecule that is used to study both facets of the cellular immune response. Using mass spectrometry analysis of complex HLA-bound peptide pools isolated from large amounts of HLA-B*2705+ cells, we identified 200 naturally processed HLA-B*2705 ligands. Our analyses revealed that a change in the position (P) 2 anchor motif was detected in the 3% of HLA-B*2705 ligands identified. B*2705 class I molecules were able to bind these six GlnP2 peptides, which showed significant homology to pathogenic bacterial sequences, with a broad range of affinities. One of these ligands was able to bind with distinct conformations to HLA-B27 subtypes differentially associated with ankylosing spondylitis. These conformational differences could be sufficient to initiate autoimmune damage in patients with ankylosing spondylitis-associated subtypes. Therefore, these kinds of peptides (short, with GlnP2, and similar low affinity to all HLA-B27 subtypes tested but with unlike conformations in differentially ankylosing spondylitis-associated subtypes) must not be excluded from future researches involving potential arthritogenic peptides.
In-substrate-bitline sense amplifier with array-noise-gating scheme for low-noise 4F2 DRAM array operable at 10-fF cell capacitance

An in-substrate-bitline sense amplifier (SA) with an array-noise-gating (ANG) scheme—for stable sensing operation in a 4F2 DRAM array with cell capacitance of under 20 fF—is proposed. A circuit simulation assuming 40-nm-class 4F2 DRAM chip shows that the SA reduces noise by 58% compared to a conventional SA and achieves stable sensing operation even at cell capacitance of 10 fF.
Effect of Local Synaptic Strengthening on Global Activity-Wave Growth in the Hippocampus

Analysis of a continuum model of the hippocampus shows that strengthening of the synaptic connections within localized regions can convert the global activity-wave properties from decay to growth. These growing waves can play a part in the implantation of long-term memory in the higher brain regions. The wavelength of the fastest-growing mode decreases with increasing local synaptic strength and can be modified by the chemical state as reflected by synaptic sensitivity to stimuli. The temporal period of the response is a constant, equal to twice the delay time exhibited by some of the hippocampal inhibitory neurons (“d-cells”). The value for the period obtained from this relationship and measurement of the delay time agrees with the hippocampal gamma rhythm. For normal hippocampal function the proportion of d-cells is limited to one-third the total number of inhibitory neurons.
Corynebacterium coyleae sp. nov., isolated from human clinical specimens.

Over a 5-year period, six isolates of a previously unknown nonlipophilic coryneform bacterium were isolated from human clinical specimens. The most characteristic phenotypic reactions of these isolates included slow fermentative acid production from glucose but no acid production from maltose and sucrose and a strongly positive CAMP reaction. Chemotaxonomic investigations revealed that meso-diaminopimelic acid and mycolic acids were present, that palmitic, oleic, and stearic acids were the predominant cellular fatty acids, and that the G + C content was 62 to 64 mol%, characteristics which are consistent with assignment to the genus Corynebacterium. Phenotypically, the unknown coryneform bacterium could be readily differentiated from all other Corynebacterium species. A 16S rRNA gene sequence analysis and quantitative DNA-DNA hybridization experiments demonstrated unambiguously that the unknown coryneform bacterium is a member of the genus Corynebacterium and is genotypically distinct from all other members of this genus. Based on phenotypic and genotypic findings, a new species, Corynebacterium coyleae sp.nov., is proposed. The type strain of C coylease is strain DSM 44184 (= CCUG 35014).
Dual band antenna using the substrate integrated waveguide as an Epsilon Negative transmission line

The substrate integrated waveguide (SIW) is analyzed as an Epsilon Negative transmission line for the design of dual band dual mode antennas. The dual band design is feasible by exciting an open ended SIW to produce the zeroth order resonance (ZOR) or infinite wavelength mode at the cutoff frequency where a zero permittivity point is presented, and the first order resonance occurring at a frequency where the length of the waveguide is a half of the guided wavelength. A new design procedure is demonstrated using the theoretical analysis of the SIW. A miniaturized dual band antenna working at 10/17 GHz frequency bands is implemented and characterized. The proposed design procedure has been confirmed. The antenna features a compact size of 0. 35λ0 × 0. 2λ0 at 10 GHz.
The effects of mirror therapy on the gait of subacute stroke patients: a randomized controlled trial

Objective: To investigate the effect of mirror therapy on the gait of patients with subacute stroke. Design: Randomized controlled experimental study. Setting: Outpatient rehabilitation hospital. Subjects: Thirty-four patients with stroke were randomly assigned to two groups: a mirror therapy group (experimental) and a control group. Interventions: The stroke patients in the experimental group underwent comprehensive rehabilitation therapy and mirror therapy for the lower limbs. The stroke patients in the control group underwent sham therapy and comprehensive rehabilitation therapy. Participants in both groups received therapy five days per week for four weeks. Main measures: Temporospatial gait characteristics, such as single stance, stance phase, step length, stride, swing phase, velocity, and cadence, were assessed before and after the four weeks therapy period. Results: A significant difference was observed in post-training gains for the single stance (10.32 SD 4.14 vs. 6.54 SD 3.23), step length (8.47 SD 4.12 vs. 4.83 SD 2.14), and stride length (17.03 SD 6.57 vs 10.54 SD 4.34) between the experimental group and the control group (p < 0.05). However, there were no significant differences between two groups on stance phase, swing phase, velocity, cadence, and step width (P > 0.05). Conclusion: We conclude that mirror therapy may be beneficial in improving the effects of stroke on gait ability.
Brain tumor diagnosis systems based on artificial neural networks and segmentation using MRI

Automatic defects detection in Magnetic Resonance Images (MRI) is a crucial factor in several diagnostic applications. This paper presents an intelligent Neural Networks (NN) and segmentation-based system to automatically detect and classify various brain tumors types that might be depicted in MRI. The proposed intelligent system is divided into two main parts: the first part is composed of hybrid neural networks composed of the Principal Component Analysis (PCA) for dimensionality reduction to extract the global features of the MRI cases. The second part is based on the segmentation of the MRI cases using the Wavelet Multiresolution Expectation Maximization (WMEM) algorithm to extract the local features of the cases. Then Multi-Layer Perceptron (MLP) is applied to classify the extracted features from either the first part or from the segmentation process. A comparison study between the performances of MLP when one accomplished the two approaches. The purpose of this research is to save the radiologist time, increases accuracy, and so helps non-experts doctors in diagnosing brain tumors.
Deoxyribonucleoside Phosphoramidites

The detailed preparation of deoxyribonucleoside phosphoramidites bearing a 4‐[N‐methyl‐N‐(2,2,2‐trifluoroacetyl)amino]butyl group for P(III) protection is presented. The use of this group circumvents nucleobase alkylation during oligonucleotide deprotection. Two syntheses of phosphoramidites starting from either a phosphordichloridite precursor or a bis‐(N,N‐diisopropylamino)chlorophosphine intermediate are described for the phosphinylation of suitably protected deoxyribonucleosides.
Quantitation of hepatic glucose fluxes and pathways of hepatic glycogen synthesis in conscious mice.

Mice were studied with the euglycemic hyperinsulinemic and the hyperglycemic clamp techniques after a 6-h fast: 1) euglycemic (6.7 +/- 0.2 mM) hyperinsulinemia (approximately 800 microU/ml); 2) hyperglycemic (15.3 +/- 0.4 mM) hyperinsulinemia (approximately 800 microU/ml). All mice received an infusion of [3-3H]glucose and [U-14C]lactate. Basal hepatic glucose production (HGP) averaged approximately 170 mumol.kg-1.min-1 in both groups. During euglycemic and hyperglycemic hyperinsulinemia, HGP decreased by 53% (to 76.7 +/- 11.1 mumol.kg-1.min-1; P < 0.01) and 74% (to 43.3 +/- 7.2 mumol.kg-1.min-1; P < 0.01), respectively. Hyperglycemia increased glucose cycling (by 2.1-fold; P < 0.01) and the contribution of gluconeogenesis to HGP (88 vs. 43%; P < 0.01) while decreasing that of glycogenolysis (12 vs. 57%; P < 0.01). The percentage of neosynthetized hepatic glycogen formed via the direct pathway was markedly increased during hyperglycemia (53 +/- 2% vs. 23 +/- 3%; P < 0.01): These data indicate that the assessment of hepatic glucose fluxes can be accomplished in conscious unrestrained mice and that, in the presence of hyperinsulinemia, hyperglycemia causes 1) a further inhibition of HGP mainly via inhibition of glycogenolysis and increase in hepatic glucose cycling; and 2) about a fivefold stimulation in the direct pathway of hepatic glycogen formation.
The Soft $\hbox{Punchthrough}+$ Superjunction Insulated Gate Bipolar Transistor: A High Speed Structure With Enhanced Electron Injection

The aim of this paper is to demonstrate the application of the superjunction (SJ) design in an insulated gate bipolar transistor (IGBT). Bipolar conduction is present and enhanced at the cathode side of the device, while the p-pillars collect the plasma deep from the anode side, thus significantly enhancing its turn-off speed. The disconnected soft punchthrough + (SPT+) SJ IGBT is similar to the SJ IGBT, which we have previously reported, but the drift region pillars do not extend up to the cathode contact. Instead, the upper part of this device is similar to the SPT+ IGBT, i.e., it features an n+ injector around the p-well and the n-drift region that is lightly doped. The improvement in the overall performance is impressive (25% lower ON-state losses and 30% lower switching losses) and can indeed justify the technology cost associated with the SJ technology. We also demonstrate how this technology can be used to form a snapback-free reverse conducting IGBT.
Cutaneous and renal glomerular vasculopathy in a great dane resembling ‘Alabama rot’ of greyhounds

fil)rils (-SAE). NcPuropllitology( .nti Applic'd Ncirobiolugy 14, 325-336 11ILLlEER, J.M., JENNY, A. L., TAYLOR, W5. D., RACE, R. E., ERNS, L). R. , KATZ, J. B. & RLUBINS' 'EIN, R. 1994) D)etection of prion proteini in formiialin-fixed brain bNs hs drated autoclaving imllmUnohistochernistry for the diagnlosis of scrapic in sheep. Jouira1()l of ' tcrilnarr L)iagnostic hil,cstigation 6, 366-368 OIE (2000) Bovine spongifornii encephalopathy. In MlanlLial of Stanldards for I)i.agnostic Tests anid accicnes. 4th edni. Paris, Office Ilternlatiolnal des [pizooties. pp 457-466 ORGE, 1. , SINMAS, J. P., FERNAND)ES, A. C. , RAMOS, M. & (ALO, A. (20(0() Similarits of the lesioni profile of lSt3 in PortuLguLese cattle to that described in 13ritish cattle. X tceriltiary Rccord 147, 486-488 SC1IRLUDER, B. E. , VAN KEUI EN, L. J., N RONIANS, N1. E. , LANGEVELD, J. P. & SMNIFS, NI. A. ( 1998) loilsillar hiopsy and PrP5 detectioll in the prcclinical diagniosis of scrapie. Xtcrieoniry Record1 142, 564-568 SIMMN1ONS, NI. Ni. , HARRIS, P., JE1 FREY, NI. , MEt K, S. C(.,131 AMIRE, 1. W'. & WELLS5, G. A. (1996) iSFt in (reat Britaini: consistencs of the necirohistopatlhological finidinigs ill tvso random annlLual samiiples of clihnicalls stispect cases. kieteriiii 1IRecor(i 138, 75177 NAN KFULEN, L. 1. NI., SCHREUI)ER, B. E. (C., MIFIOEN, R. H., POElENAN l)EN BER(G, NI., M1OO-HARKES, G., N RONMANS, NI. U. \W. & LANENVELD, J. P. NI. (1995) Imnll1tI1nohi0stochenical detectioin anid localizationl of prioni protein in hi ai tissLeCof sheep wvith natuiral scrapie. X'erirlno Pathology 32, 299-308 WNELIS, (,. A. H., HANCOC K, I. D). , COOLFE, \. A. ,RICHARDS,M1s S. , HI(,G,INS, R. J. & I)AVID), (G. P. 1989) Bovinse spongifornii encephalopathy: diagnostic signaificance of s acLolar chaniges in selcctet nLICiei of the rnledUll ohlongata. S'cteritityrlr RcKord 125, 521 -'24
The Influence of Myosin Heavy Chain Isoform Composition and Training Status on the Patterns of Responses for Mechanomyographic Amplitude versus Isometric Torque

The purpose of this study was to examine the influence of myosin heavy chain (MHC) isoform composition and training status on the mechanomyographic (MMG) amplitude versus isometric torque relationship for the vastus lateralis. Five resistance-trained (mean ± SD age = 23.2 ± 3.7 years), 5 aerobically trained (mean ± SD age = 32.6 ± 5.2 years), and 5 sedentary (mean ± SD age = 23.4 ± 4.1 years) men performed isometric muscle actions of the leg extensors in 20% increments from 20% to 100% of the maximum voluntary contraction. Biopsies from the vastus lateralis revealed that the MHC composition for the resistance-trained subjects was 59.0 ± 4.2% Type IIa, 0.1 ± 0.1% Type IIx, and 40.9 ± 4.3% Type I. The aerobically-trained subjects had 27.4 ± 7.8% Type IIa, 0.0 ± 0.0% Type IIx, and 72.6 ± 7.8% Type I MHC. The sedentary subjects had 42.1 ± 7.8% Type IIa, 17.8 ± 6.4% Type IIx, and 40.1 ± 10.9% Type I MHC. There were no consistent patterns of responses for the resistance-trained, aerobically trained, or sedentary subjects for MMG amplitude versus torque. Thus, differences in MHC isoform composition and training status did not explain the unique torque-related patterns for MMG amplitude.
Modeling and Tracking Surface Instructional Discourse Dynamics

In this work we focus on classroom discourse. Specifically, we describe an approach to modeling and tracking the classroom verbal interaction between teacher and students. We assume that the evolution of the classroom discourse takes place in a space whose dimensions correspond to specific discourse categories and thus the rate of occurrence of these events can be monitored, categorized and tracked. In other words, we assume that the teacher relies on a collection of verbal mechanisms in guiding the classroom discussion. The speed and effectiveness with which the discourse progresses in these dimensions (or reacts to the teacher stimuli) is thus controlled by the teacher's actions. We propose a dynamical system representation (linear Discrete Wiener Process Acceleration model under system and observation noise) to model the classroom interaction. This model can be used to track discourse, and to predict and smooth discourse trajectories with applications to problem solving, conversational analytics, dialog understanding, etc.
Ethyl N-phenyloxamate.

The oxamate group in the title compound, C(10)H(11)NO(3), is almost coplanar with the phenyl ring because of intramolecular hydrogen-bonding interactions, and the structure can be described as an anilide single bonded to an ethyl carboxylate group. The supramolecular structure is achieved through intermolecular hard N-H.O and soft C-H.X (X = O and phenyl) hydrogen-bonding interactions.
An opto-VLSI reconfigurable broad-band optical splitter

A reconfigurable broad-band optical splitter is presented, which uses the multicasting capability of opto-very-large-scale-integrated (Opto-VLSI) technology to adaptively split an optical signal to N fiber ports. We demonstrate the proof-of-principle of a three-port structure that uses a reconfigurable Opto-VLSI processor to adaptively multicast an input optical signal with dynamic attenuation range of more than 25 dB over 55-nm bandwidth.
RIAPPA: a Robust Identity Assignment Protocol for P2P overlays

Peer-to-peer (P2P) overlay networks have been proposed to solve routing problems of big distributed infrastructures, even for Internet scale. But the research community has been questioning the security of these networks for years. Most prior work in security services was focused on trust and reputation systems, anonymity, and secure routing. However, the proper management of identities in overlays is an important prerequisite to provide most of these security services. In this paper, we propose a protocol to control the access to a P2P overlay and to assign identities in a secure way; all this preserving the anonymity of users. This protocol involves two trusted third parties (TTPs), thanks to which it is possible to preserve the users’ anonymity within the network without losing traceability. Users are authenticated by a TTP using real-world digital certificates, they select their network identifier jointly with the other TTP, and finally, the two TTPs issue the internal certificate to them. The protocol also provides revocability and protection against Sybil attacks, Eclipse attacks, whitewashers, and so on. A detailed protocol description is presented, and a performance and security analysis of the protocol is also provided. Copyright © 2014 John Wiley & Sons, Ltd.
Antigenic analysis of prototype influenza A (H3N2) strains by the antiserum absorption method

SUMMARY Prototype strains of the influenza A (H3N2) virus can be arranged on a gradient showing the degree of the antigenic drift which the haemagglutinins of the strains have undergone. The demonstration of fine antigenic differences is based on an antiserum absorption test which allows a detailed antigenic analysis of strains. The gradient provides information on variation in strains occurring in different geographical areas and its use may be helpful in differentiating between introduced strains and locally developing variants.