Miracle-dz/UniFAR-FTUs huggingface dataset:
A 3D building blocks approach to analyzing and predicting structure of proteins

A new approach is introduced for analyzing and ultimately predicting protein structures, defined at the level of Cα coordinates. We analyze hexamers (oligopeptides of six amino acid residues) and show that their structure tends to concentrate in specific clusters rather than vary continuously. Thus, we can use a limited set ofstandard structural building blocks taken from these clusters as representatives of the repertoire of observed hexamers. We demonstrate that protein structures can be approximated by concatenating such building blocks. We have identified about 100 building blocks by applying clustering algorithms, and have shown that they can “replace” about 76% ofall hexamers in well‐refined known proteins with an error of less than 1 Å, and can be joined together to cover 99% of the residues. After replacing each hexamer by a standard building block with similar conformation, we can approximately reconstruct the actual structure by smoothly joining the overlapping building blocks into a full protein. The reconstructed structures show, in most cases, high resemblance to the original structure, although using a limited number of building blocks and local criteria of concatenating them is not likely to produce a very precise global match. Since these building blocks reflect, in many cases, some sequence dependency, it may be possible to use the results of this study as a basis for a protein structure prediction procedure.
Vortex Pinning Properties of Dense Ti-Doped MgB2 Bulks Sintered at Different Temperatures

We have studied the trapped field by field-cooled magnetization and microstructure of the Ti-doped MgB<sub>2</sub> bulks fabricated at 700°C by an in situ hot isostatic pressing method, which were compared with those at 900°C. The maximum trapped field B<sub>T</sub> of 3.0 T at 19 K was realized at the Ti-doping level of 10%-20%. In spite of the lower filling factor of 700°C Ti-doped bulks, i.e., f ~80%, the obtained B<sub>T</sub> = 3.0 T was 1.3 times larger than that of the nondoped bulk (f ~ 90%) and was comparable with those for the 900°C Ti-doped bulks (f ~ 90%) with the same Ti contents. The quantitative analysis of the chemical composition revealed that fine particles of higher borides, i.e., MgB<sub>y</sub> (y > 2), existed in the MgB<sub>2</sub> matrix. The low sintering temperature of 700°C and the Ti doping strongly suppressed the grain growth of the MgB<sub>2</sub> matrix. The increase in both the grain boundaries of MgB<sub>2</sub> and the nonsuperconducting fine particles enhanced the trapped field of the present 700°C Ti-doped MgB2 bulks.
The nature of bipolar disorder.

The underlying pathophysiology of bipolar disorder is a continually evolving complexity of multilayer interacting and independent systems. The dearth of adequate preclinical or clinical models that incorporate the various features of the illness, i.e., acute and chronic, recurrent and episodic, and time-course and treatment-related variables, has made the consistency and interpretation of data difficult. Newer technologies and the availability of structurally and mechanistically distinct pharmacologic agents have expanded opportunities for experimental study. In addition to the well-known neurotransmitter systems that are disrupted in mood disorders, critical guanine nucleotide-binding protein (G protein)-coupled signaling pathways are implicated in modulating mood state. Regulation of gene expression and identification of factors regulating neuroplasticity and neurotrophic events in the central nervous system in bipolar disorder are 2 of the more recent approaches contributing to clarification of the pathophysiology and potential treatment options.
Counting Casualties in the War on Prisoners

OVER THE LAST SEVERAL DECADES, numerous prisons in the United States have operated in a state of crisis.1 The sheer number of persons incarcerated during these years overwhelmed the capacity to safely and humanely house and administer to the prisoners placed under correctional control. Policies of mass incarceration that were pursued over these decades created drastic shortages of space and resources. Unwieldy numbers of prisoners were largely warehoused with little to do. Although some states took meaningful steps designed to address the causes of their overcrowding crisis, others—such as California—did not. As a result, prisoners have continued to be released back into many communities with a range of unmet needs and, in some instances, a host of serious problems that remained unaddressed
Influence of Auxins and Sucrose in Monoterpenoid Oxindole Alkaloid Production by Uncaria tomentosa Cell Suspension Cultures

Growth and alkaloid production in Uncaria tomentosa cell suspension cultures were studied in Murashige and Skoog medium supplemented with 10 μM 2,4‐dichlorophenoxyacetic acid, 10 μM kinetin, and 58 mM sucrose for maintenance and with 10 μM indole‐3‐acetic acid, 10 μM kinetin, and 58 mM sucrose for production. A U. tomentosa pale Uth‐3 cell line, cultured in the production medium, showed a reduced lag phase and a specific growth rate (μ) of 0.27 day−1, while cells growing in the maintenance medium showed μ = 0.20 day−1. U. tomentosacells growing in the production medium produced monoterpenoid oxindole alkaloids (MOA) in amounts of 10.2 ± 1.6 μg g−1 dry weight (DW). The chemical profile of MOA produced by in vitro cell cultures was similar to that found in the plant. After 10 subcultures, maximum MOA production decreased to 2.0 ± 0.7 μg g−1 DW, while tryptamine alkaloids (TA) were produced with a maximum of 6.2 ± 0.4 μg g−1 DW. The increase of initial sucrose concentration up to 145 mM in the production medium enhanced the cell biomass by 3.2‐fold (from 10.2 ± 0.1 to 32.8 ± 1.1 g DW L−1), reduced μ from 0.27 to 0.23 day−1, and provoked a substantial accumulation of TA (23.1 ± 4.7 μg g−1 DW). A high sucrose concentration stimulated MOA production in the maintenance medium (2.7 ± 0.5 μg g−1 DW), even in the presence of 2,4‐dichlorophenoxyacetic acid.
National, state, and urban area vaccination coverage levels among children aged 19-35 months--United States, 1998.

PROBLEM/CONDITION High vaccination levels in the population are necessary to decrease disease transmission and prevent disease; therefore, an important component of the U.S. vaccination program is the assessment of vaccination coverage. Current goals are for > or = 90% coverage with recommended vaccines during the first 2 years of life. REPORTING PERIOD January-December 1998. DESCRIPTION OF SYSTEMS The National Immunization Survey (NIS) is an ongoing, random-digit-dialed telephone survey that gathers vaccination coverage data for children aged 19-35 months in all 50 states and 28 urban areas. Vaccination coverage rates derived from NIS data are adjusted statistically for households with multiple telephone lines, household nonresponse, the proportion of households without telephones, and vaccination provider nonresponse. The results were also adjusted to match the known total population of children in each survey area. RESULTS On the basis of NIS data, national coverage was > or = 90% for three doses of poliovirus vaccine (Polio), three doses of Haemophilus influenzae type b vaccine (Hib), and one dose of measles-containing vaccine (MCV). Coverage was the highest ever reported for four doses of any diphtheria and tetanus toxoids and pertussis vaccine (DTP) (i.e., diphtheria and tetanus toxoids and pertussis vaccine, diphtheria and tetanus toxoids [DT], or diphtheria and tetanus toxoids and acellular pertussis vaccine [DTaP]) (83.9%), three doses of hepatitis B vaccine (Hep B, 87.0%), and one dose of varicella vaccine (43.2%). The number of states achieving the > or = 90% goal was 47 for three doses of Hib, 40 for three doses of Polio, 40 for one dose of MCV, nine for three doses of Hep B, and seven for four doses of DTP. Proportionally fewer urban areas achieved the > or = 90% goal: 23 of 28 for three doses of Hib, 13 for three doses of Polio, 16 for one dose of MCV, five for three doses of Hep B, and one for four doses of DTP. No state or urban area has yet achieved the > or = 90% goal for varicella. INTERPRETATION Findings from the 1998 NIS indicate that national vaccination coverage levels for routinely recommended childhood vaccines are at the highest levels ever reported. However, substantial variation in coverage remains at the state and urban area levels. PUBLIC HEALTH ACTIONS The public health community and vaccination providers in areas with low coverage should intensify their efforts to implement recommended strategies for increasing vaccination coverage to ensure that children are equally well protected throughout the United States.
Channel codes that exploit the residual redundancy in CELP-encoded speech

We consider the problem of reliably transmitting CELP-encoded speech over noisy communication channels. Our objective is to design efficient coding/decoding schemes for the transmission of the CELP line spectral parameters (LSPs) over very noisy channels. We begin by quantifying the amount of "residual redundancy" inherent in the LSPs of Federal Standard 1016 CELP. This is done by modeling the LSPs as first- and second-order Markov chains. Two models for LSP generation are proposed; the first model characterizes the intraframe correlation exhibited by the LSPs, while the second model captures both intraframe and interframe correlation. By comparing the entropy rates of the models thus constructed with the CELP rates, it is shown that as many as one-third of the LSP bits in every frame of speech are redundant. We next consider methods by which this residual redundancy can be exploited by an appropriately designed channel decoder. Before transmission, the LSPs are encoded with a forward error control (FEC) code; we consider both block (Reed-Solomon) codes and convolutional codes. Soft-decision decoders that exploit the residual redundancy in the LSPs are implemented assuming additive white Gaussian noise (AWGN) and independent Rayleigh fading environments. Simulation results employing binary phase-shift keying (BPSK) indicate coding gains of 2-5 dB over soft-decision decoders that do not exploit the residual redundancy.
Performance of an implantable printed folded dipole antenna for biomedical wireless communication

In this study, an implantable compact printed folded dipole antenna functioning in the Medical Implant Communication Service (MICS) frequency band (402 - 405 MHz) is proposed. The developed antenna, exhibiting dimensions of 19.6 * 2 * 0.254 mm3, is embedded into the skin and muscle tissues of a canonical head and trunk model, respectively. Antenna is easily tuned when implanted into the different phantoms. Resonance and radiation characteristics inside the tissue-simulating mediums are assessed and a communication link between the implanted antenna and an external module is established.
Streptococcal M6 protein binds to fucose-containing glycoproteins on cultured human epithelial cells

M6 protein of Streptococcus pyogenes binds directly to HEp-2 cell surfaces and helps to mediate bacterial adhesion. Two epithelial cell receptors for M protein were identified as 97- and 205-kDa glycoproteins. Purified recombinant M6 protein (rM6) showed a dose-dependent and saturable binding to isolated HEp-2 membranes in an enzyme immunoassay. The HEp-2 cell receptors were selectively denatured by pretreatment of isolated membranes at 80 degrees C or with chymotrypsin; binding activity for rM6 was reduced 83 and 80%, respectively. Pretreatment of the HEp-2 membranes with neuraminidase-N-glycosidase, neuraminidase-O-glycosidase, alpha-L-fucosidase, or Ulex lectin caused 33, 42, 73, and 80% reduction of rM6 binding, respectively. Quantitative analysis of HEp-2 cells pretreated with alpha-L-fucosidase showed that the 97- and 205-kDa glycoproteins lost 70 and 62% of their abilities to bind M6 protein and that 33% of the HEp-2 cell's ability to bind whole streptococci was also lost. These results indicated that binding of M6 protein to HEp-2 cell surfaces is highly selective for certain fucose-containing oligosaccharides on these glycoproteins.
Separating live from dead longleaf pine seeds: good and bad news

Of all southern pine seeds, longleaf pine (Pinus palutris Mill.) are the most difficult to collect, process, treat, and store while maintaining good seed quality. As a result, interest in techniques for separating filled dead from live longleaf pine seeds has developed. The good news is that new technologies are becoming available to evaluate seed quality, but the bad news is that they seem to have limited application to longleaf pine. Tests suggest that incubating, drying, and separating, chlorophyll fluorescence, and near infrared techniques do not help improve longleaf pine seed quality. The incubating-drying-separating method is inefficacious because variability in the seed coat wing stub affects seed flotation. The chlorophyll fluorescence method measures changes in chlorophyll content as seeds mature or are damaged, but such changes do not seem to occur in pine seeds. The near infrared method seems to offer the best potential. The use of near infrared scanning technologies can determine changes in seed constituents, but we have not been able to determine which measurable seed constituents may change as viability declines.
Conceptual design of shapes in Virtual Environments through the re-use of heterogeneous data

Today, digital data such as 2D images, 3D meshes and 3D point clouds are widely used to design Virtual Environments (VE). Most of the time, only one type of those multimodal data is used to describe and specify the shapes of the objects. However, a single object can be seen as a combination of components linked with constraints specifying the relationships and the rigid transformations defining their arrangement. Thus, the definition of news methods able to combine any kind of multimodal data in an easy way would allow nonexperts of VE to rapidly mock-up objects and scenes. In this paper, we propose a new shape description model together with its associated constraints toolbox enabling the description of complex shapes from multimodal data. Not only rigid transformations are considered but also scale modifications according to the specified context of the constraint setting. The heterogeneous virtual objects (i.e. composed by scalable multimodal components) then result from the resolution of a constraint satisfaction problem through an optimization approach. The proposed approach is illustrated with examples obtained with our prototype software.
‘Autonomic conflict’: a different way to die during cold water immersion?

Abstract Cold water submersion can induce a high incidence of cardiac arrhythmias in healthy volunteers. Submersion and the release of breath holding can activate two powerful and antagonistic responses: the ‘cold shock response’ and the ‘diving response’. The former involves the activation of a sympathetically driven tachycardia while the latter promotes a parasympathetically mediated bradycardia. We propose that the strong and simultaneous activation of the two limbs of the autonomic nervous system (‘autonomic conflict’) may account for these arrhythmias and may, in some vulnerable individuals, be responsible for deaths that have previously wrongly been ascribed to drowning or hypothermia. In this review, we consider the evidence supporting this claim and also hypothesise that other environmental triggers may induce autonomic conflict and this may be more widely responsible for sudden death in individuals with other predisposing conditions.
QSPR checking and validation: a case study with hydroxy radical reaction rate constant

Traditionally, QSAR and QSPR models have been fitted by splitting the available compounds into separate learning and validation sets. The model is then fitted to the learning set and assessed using the validation set. Cross-validation (CV) uses all available compounds for both purposes, so that the full body of available information is brought to bear on both the learning and the validation portions of the study. The price paid for this additional information is a substantially greater computational load. A common mistake in using CV is to omit some of the repetitive computations. This mistake leads to substantial bias in the assessment. A hydroxyl radical reaction rate dataset is used to illustrate the superiority of CV and the pitfalls from its improper execution when modeling using nearest neighbors, paralleling behavior in the well-studied linear model setting.
SOI Devices and Technology

SOl technology for state-of-the-art CMOS technology is rapidly approaching maturity. PD-SOl device design has the advantage of easier manufacturing but requires mQre sophisticated device and circuit design to reduce the effects of the floating body. FD­ SOl device design potentially has the advantage of no floating-body effects but requires very thin silicon films making manufacturing more challenging. Besides providing a boost in performance relative to bulk at any one CMOS technology node, SOl also offers new overall lC architecture possibilities that increasingly exploit the third dimension in unique ways. These include double-gate MOSFET'sfor increased current drive density and/or dynamic VT control, substantial increase in usable levels of interconnect, and 3-D lC implementation.
Determination and depletion of amoxicillin residues in eggs

Eggs were used to study the determination and depletion of amoxicillin (AMO) residues after oral dosing hens (25.0 mg kg–1, 50.0 mg kg–1 body weight), once daily for five days. A reverse-phase high-performance liquid chromatography with fluorescence detection (RP-HPLC-FLD) method was developed to determine AMO residues in albumen, yolk and whole egg. By using pre-column derivatisation, an improved liquid–liquid extraction procedure was developed for sample preparation. AMO were extracted from eggs with acetonitrile. The extract solution was extracted using saturated methylene chloride. The supernatant was reacted with salicylaldehyde under acidic and heating conditions. Limits of detection (LODs) were 1.2 ng g–1 and limits of quantification (LOQs) were 3.9 ng g–1 for AMO. Recoveries of AMO from samples fortified at levels of 5.0–125.0 ng g–1 ranged from 79.1% to 88.5% in albumen, 78.6–83.6% in yolk and 78.3–85.1% in whole egg, with coefficients of variation of ≤7.3%. The maximum concentrations of AMO in albumen, yolk and whole egg were found to occur at 1.5, 2.5, 1.5 days after withdrawal of medication respectively. AMO was not detectable in albumen at 7.5 days after final administration of AMO, at 10.5–11.5 days in yolk and 10.5 days in whole egg after administration of two oral doses. The method was applied during the residue study of AMO in order to formulate a reasonable withdrawal period to ensure food safety.
Incident Management Optimization through the Reuse of Experiences and Natural Language Processing

Information Technology (IT) Governance need for tools and processes that assist the qualification, retention and reuse of solutions to leverage the management of incidents. In this sense, this work proposes a process for resolving incidents, whose differential is the use of CBR (Case Based Reasoning) and NLP (Natural Language Processing) techniques, aiming the reuse of experience in handling similar incidents. Specially, NLP techniques, such as morph syntactic analysis and semantic textual similarity, are used in the retrieval phase of the CBR system. We applied the proposed process in a real scenario after the deployment of an ERP system in a mixed capital company, in order to validate if the use of CBR and NLP components in an Incident Management Process optimizes the handling of incidents.
Selective Leakage of Host‐Cell Proteins during High‐Cell‐Density Cultivation of Recombinant and Non‐recombinant Escherichia coli

Significant leakage of host‐cell proteins into the culture medium occurred during high‐cell‐density cultivation of E. coli. Identification of these medium proteins revealed almost exclusively a periplasmic origin. Release of periplasmic proteins into the culture medium was observed throughout the entire cultivation of recombinant or non‐recombinant cells. Leakage was intensified, however, in the final part of high‐cell‐density cultures (>100 g L−1 dry cell mass) or when a temperature upshift was used for induction of recombinant protein synthesis. After temperature upshift, formation rates and residual cellular concentrations of periplasmic proteins declined with individual rates; e.g., the cellular content of the large periplasmic dipeptide binding protein DppA (57.4 kDa) started to decline about 4 h after the temperature upshift, whereas the smaller periplasmic d‐galactose/d‐glucose binding protein MglB (33.4 kDa) was already lost during the first hour after the upshift. In addition to periplasmic proteins, the osmotic‐shock‐sensitive heat‐shock protein DnaK was found in significantly higher proportion in the cell‐free medium of the temperature‐challenged culture than other cytoplasmic proteins. Cell lysis was not observed even after prolonged cultivation. Thus, loss of a subset of cellular proteins of mainly periplasmic origin ordinarily occurs during cultivation and is intensified through stressful conditions in high‐cell‐density cultures. The selective release of cellular proteins of periplasmic origin offers the opportunity to simplify the downstream processing of recombinant proteins directed to the periplasm of E. coli.