gebhart/patrepeval huggingface dataset:
Multiplexed short tandem repeat polymorphisms of the Weber 8A set of markers using tailed primers and infrared fluorescence detection (1998)

Short tandem repeat polymorphism (STRP) markers have become important reagents for mapping genetic diseases. These markers are available as screening sets, which are located in all chromosomes at discrete intervals, allowing the entire genome to be analyzed. Mapping studies that include many individuals in the analysis necessitate the production of large numbers of genotypes. In an effort to increase the efficiency and lower the cost of using these STRP screening sets, we have divided the amplification primers of the Weber 8A screening set into groups that can be amplified in single polymerase chain reaction (PCR) amplification reactions, resulting in a reduction of both time and cost. Fluorescently-labeled amplification products were produced using a three primer reaction. The forward STRP amplification primer for each marker contained a 19 bp sequence at the 5' end. A fluorescently-labeled primer, with a sequence identical to the 19 bp tail, was added to the amplification reaction as the sole source of fluorescent label. The STRP banding pattern is detected using an automated fluorescent DNA sequencer. Use of this multiplexed genomic screening set should greatly enhance the mapping of human disease loci.
Structure of the human FERRY Rab5 effector complex (2021)

Abstract Long-range mRNA transport is crucial for the spatio-temporal regulation of gene expression, and its malfunction leads to neurological disorders. The pentameric FERRY Rab5 effector complex is the molecular link between mRNA and early endosomes in mRNA intracellular distribution. Here, we determine the cryo-EM structure of the human FERRY complex, composed of Fy-1 to Fy-5. The structure reveals a clamp-like architecture, where two arm-like appendages of Fy-2 and a Fy-5 dimer, protrude from the central Fy-4 dimer. The coiled-coil domains of Fy-2 are flexible and project into opposite directions from the core. While the Fy-2 C-terminal coiled-coil acts as binding region for Fy-1/3 and Rab5, both coiled-coils and Fy-5 concur to bind mRNA. Mutations causing truncations of Fy-2 in patients with neurological disorders impair Rab5 binding or FERRY complex assembly. Thus, Fy-2 serves as a binding hub connecting all five complex subunits and mediating the binding to mRNA and early endosomes via Rab5. The FERRY structure provides novel mechanistic insights into long-distance mRNA transport.
The effect of surface treatment of denture acrylic resin on the residual monomer content and its release into water (1996)

The test specimens were processed by autopolymerizing poly(methylmethacrylate) (PMMA), and their surfaces were untreated, polished in a conventional manner with a rag wheel, or coated with a light-curing resin. The residual methylmethacrylate (MMA) content and its release into water from the specimens were measured with high-performance liquid chromatography. The light-curing resin coating reduced most effectively the release of residual MMA into water during a 2-day storage, but conventional polishing of the PMMA surface had a similar effect when the mean values of groups were tested by means of one-way ANOVA (p < 0.001). The residual MMA content was lowest in the test specimens coated with a light-curing resin, whereas only a slight difference was seen when the untreated and polished test specimens were compared. This study suggests that not only light-curing resin coating but also the conventional polishing of the denture PMMA reduces residual MMA release into water in vitro.
Tissue transformation into bone in vivo. A potential practical application (1991)

The transformation of mesenchymal tissue, such as muscle, into cartilage and bone can be induced by the recently purified osteoinductive factor, osteogenin, and by its parent substratum, demineralized bone matrix. We investigated the possibility of transforming readily available muscle flaps into vascularized bone grafts of various shapes that could be used as skeletal replacement parts. In a rat experimental model, thigh adductor muscle island flaps were placed inside bivalved silicone rubber molds. Prior to closure of the mold, 18 flaps were injected with osteogenin and coated with demineralized bone matrix. Five flaps served as controls and were injected with the vehicle only, and not coated with demineralized bone matrix. The molds were implanted subcutaneously in the rats' flanks and reopened 10 days later. The control flaps consisted of intact muscle without any evidence of tissue transformation, whereas the flaps treated with osteogenin and demineralized bone matrix were entirely transformed into cancellous bone that matched the exact shape of the mold. Using tissue transformation, we were able to generate in vivo, autogenous, well-perfused bones in the shapes of femoral heads and mandibles. (<i>JAMA</i>. 1991;266:1953-1955)
Application of Deep Learning to Underwater Invasion Warning System (2018)

In this paper, we discuss our trying to improve detection performance of a diver detection sonar using deep learning in very shallow water area. We had developed and evaluated our underwater invasion warning system to detect intruders, diver and diver with swimmer delivery Vehicle (SDV), which try to intrude a harbor for several years. We find out that there are some demand for the underwater monitoring, especially in very shallow water area, less than ten meters depth. We have already known that such very shallow water makes difficult situation for sonar operation because reverberation is high and false alarms happen frequency than usual. We have already developed better way by analyzing detection parameters such as a signal level and a signal length by a statistical analytic method and solving the problem which uses an automatic optimization method of detection parameters. But in general, it is known that there is a trade-off relation between the reducing false alarms and good detection performance. There may be case that it is difficult to combine good reducing false alarms and good detection performance by a statistical analytic method. Therefore, we have worked on development of the method to solve the problem. In this work, we discuss the detection method using deep learning as one of our trying. Like general surveillance camera, a background image will be extracted. And we will detect the moving object by subtract difference between the background image and the current image. In this paper, we developed a new algorithm to detect moving object by the same way, which employs the differences between i) the observed current plan position indication image in short PPI image and ii) the predicted PPI image generated by deep learning as a background image. The training for the predicted PPI image was executed including the reverberation in the sea. Our proposed algorithm becomes one of the new detection method which does not use the conventional method using comparison with threshold value to decrease the false detection rate.
Total Hip Arthroplasty around the Inception of the Interface Bioactive Bone Cement Technique (2016)

The long-term follow-up of THA performed around the inception of the IBBC technique has revealed low incidences of radiolucent lines, osteolysis, and revision surgery.
Calculated cross sections for electron collisions with the BeN molecule (2023)

Abstract We report a low energy electron collision calculation with the BeN molecule in its X <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msup> <mml:mi/> <mml:mn>4</mml:mn> </mml:msup> <mml:msup> <mml:mi mathvariant="normal">Σ</mml:mi> <mml:mo>−</mml:mo> </mml:msup> </mml:math> ground state using the molecular R -matrix method at a single geometry, namely, the equilibrium <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msub> <mml:mi>R</mml:mi> <mml:mi>e</mml:mi> </mml:msub> <mml:mo>=</mml:mo> <mml:mn>3.045</mml:mn> </mml:math> a 0 of the molecule. Using a suitable target model, we have calculated the elastic cross section and cross sections for electron impact excitation in several low-lying excited states of BeN. Cross sections for electron impact dissociation is derived from the electronic excitation cross sections. In addition, molecular data on bound sates of BeN and e-BeN negative ion resonances and widths at the target equilibrium R e that may be relevant for other studies are also provided.
The use of nuclear simulation calculations to support applications in radioactive tracer logging (1990)

A method for simulating the pulse height responses of passive gamma-ray spectroscopy logging tools is described, and its application to measurements of radioactive tracer spectra is demonstrated. This method consists of computing the flux at the detector surface, convolving the flux with the detector response computed in a separate step to obtain a base spectrum, convolving the base spectrum with itself to obtain a spectrum representative of the contribution due to random summing, and adding the sum spectrum to the base spectrum to obtain the final spectrum. Comparison of measured and simulated spectra and the Compton ratio derived from the measured and simulated spectra for several radioisotopes demonstrates the accuracy of the simulation method. This method has been used to compute calibration spectra for a large number of radioisotopes for which calibration measurements had not been made.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Bovine Leukemia Virus SU Protein Interacts with Zinc, and Mutations within Two Interacting Regions Differently Affect Viral Fusion and Infectivity In Vivo (2002)

Bovine leukemia virus (BLV) and human T-cell lymphotropic virus type 1 (HTLV-1) belong to the genus of deltaretroviruses. Their entry into the host cell is supposed to be mediated by interactions of the extracellular (SU) envelope glycoproteins with cellular receptors. To gain insight into the mechanisms governing this process, we investigated the ability of SU proteins to interact with specific ligands. In particular, by affinity chromatography, we have shown that BLV SU protein specifically interacted with zinc ions. To identify the protein domains involved in binding, 16 peptides distributed along the sequence were tested. Two of them appeared to be able to interact with zinc. To unravel the role of these SU regions in the biology of the virus, mutations were introduced into the env gene of a BLV molecular clone in order to modify residues potentially interacting with zinc. The fusogenic capacity of envelope mutated within the first zinc-binding region (104 to 123) was completely abolished. Furthermore, the integrity of this domain was also required for in vivo infectivity. In contrast, mutations within the second zinc-binding region (218 to 237) did not hamper the fusogenic capacity; indeed, the syncytia were even larger. In sheep, mutations in region 218 to 237 did not alter infectivity or viral spread. Finally, we demonstrated that the envelope of the related HTLV-1 was also able to bind zinc. Interestingly, zinc ions were found to be associated with the receptor-binding domain (RBD) of Friend murine leukemia virus (Fr-MLV) SU glycoprotein, further supporting their relevance in SU structure. Based on the sequence similarities shared with the Fr-MLV RBD, whose three-dimensional structure has been experimentally determined, we located the BLV zinc-binding peptide 104-123 on the opposite side of the potential receptor-binding surface. This observation supports the hypothesis that zinc ions could mediate interactions of the SU RBD either with the C-terminal part of SU, thereby contributing to the SU structural integrity, or with a partner(s) different from the receptor.
Comparison of the effects of 1,25 dihydroxyvitamin D and 25 hydroxyvitamin D on bone pathology and disease activity in Crohnʼs disease patients (2009)

According to our study, aVD has a more prominent short-term beneficial effect on bone metabolism and disease activity in CD compared with pVD.
Atomistic model of orthorhombic YBa2Cu3O7 (1988)

We have developed a rigid-ion model of the orthorhombic Y${\mathrm{Ba}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{7}$ phase. The structure of the model lattice is in good agreement with available experimental structural data. The lattice is found to be unstable at 700 K where the initiation of disordering of the oxygen ions in the copper-oxygen linear chains is observed. Vibrational properties of the lattice have been calculated and compared with the experimental vibrational density of states.
상담일반 ： 전화상담자 계속교육 요구분석 (2007)

전화상담은 모든 상담의 관문의 역할을 하기 때문에 그 질적 관리가 중요함에도 불구하고, 상담분야에서는 이를 자원봉사자들의 영역으로 인식해온 측면이 있다. 이에 따라 본 연구에서는 전화상담자들의 계속교육과 관련된 기 대를 확인하고 그 요구도상의 차이를 확인함으로써 전화상담자의 상담 능력의 질적 고양을 도모하려는데 그 목 적이 있다. 본 연구에서 설정한 연구문제는 다음과 같다. 첫째, 전화상담자들은 상담자 계속교육프로그램으로 어 떤 것을 기대하는가? 둘째, 전화상담자의 배경변인에 따라 상담 숙달도에 차이가 있는가? 셋째, 전화상담자의 배 경변인에 따라 계속교육 요구도에 차이가 있는가? 이상과 같은 문제를 파악하기 위하여 본 연구에서는 27명의 다양한 상담기관의 전화상담자들을 대상으로 인터뷰와 질문지를 통하여 예비연구를 실시하였으며, 문헌의 내용과 예비연구의 결과를 토대로 질문지를 만들어 26개 기관의 전화상담원 295명을 대상으로 설문을 실시하였다. 본 연 구의 주요 결과를 요약하면 다음과 같다. 첫째, 전화상담자의 기초교육의 내용은 일반적인 상담 이론과 기법에 치중되어 있으며, 전화상담 실제상황에서 상담자에게 부족하다고 생각되는 내용은 ``구체적인 정보제공 능력``이나 ``위기상담의 처치 및 개입기술``, ``반복전화 처리능력`` 등으로 나타났다. 또한 전화상담자들이 계속교육 내용 중에 서 가장 필요하다고 생각되는 것은 ``상담자의 정기적인 수퍼비전``과 전화상담의 고유한 특성이 있는 항목들이었 다. 둘째, 전화상담자의 직책이 높고 유급이며, 상담교육시간과 상담경력이 길수록 자신의 상담숙달도를 높게 평 가하고 있었다. 또한 3년 이상의 전화상담 경력자가 그 이하의 경력자에 비해 상담 숙달도를 높게 지각하고 있었다. 따라서 전화상담 전문성을 함양하기 위한 계속교육프로그램은 전화상담 입문단계(3년 이하의 경력)에 있는 상 담자들에게 집중적으로 제공될 필요성이 있다. 셋째, 배경변인에 관계없이 계속교육의 각 영역에 대한 요구도는 고르게 높은 편이었다. 다만 직책과 상담자 교육시간에 따라 계속교육 요구도가 차이를 보이는 영역이 있기는 하 지만, 전반적으로 배경변인에 관계없이 계속교육의 각영역에 대한 요구도는 높다고 볼 수 있다.
Vacuolating Cytotoxin of Helicobacter pylori Induces Apoptosis in the Human Gastric Epithelial Cell Line AGS (2001)

Helicobacter pylori induces cell death by apoptosis. However, the apoptosis-inducing factor is still unknown. The virulence factor vacuolating cytotoxin A (VacA) is a potential candidate, and thus its role in apoptosis induction was investigated in the human gastric epithelial cell line AGS. The supernatant from the vacA wild-type strain P12 was able to induce apoptotic cell death, whereas the supernatant from its isogenic mutant strain P14 could not. That VacA was indeed the apoptosis-inducing factor was demonstrated further by substantial reduction of apoptosis upon treatment of AGS cells with a supernatant specifically depleted of native VacA. Furthermore, a recombinant VacA produced in Escherichia coli was also able to induce apoptosis in AGS cells but failed to induce cellular vacuolation. These findings demonstrate that the vacuolating cytototoxin of H. pylori is a bacterial factor capable of inducing apoptosis in gastric epithelial cells.
Identification of a short ACE2-derived stapled peptide targeting the SARS-CoV-2 spike protein (2023)

The design and synthesis of a series of peptide derivatives based on a short ACE2 α-helix 1 epitope and subsequent [i - i+4] stapling of the secondary structure resulted in the identification of a 9-mer peptide capable to compete with recombinant ACE2 towards Spike RBD in the micromolar range. Specifically, SARS-CoV-2 Spike inhibitor screening based on colorimetric ELISA assay and structural studies by circular dichroism showed the ring-closing metathesis cyclization being capable to stabilize the helical structure of the 9-mer <sup>34</sup>HEAEDLFYQ<sup>42</sup> epitope better than the triazole stapling via click chemistry. MD simulations showed the stapled peptide being able not only to bind the Spike RBD, sterically interfering with ACE2, but also showing higher affinity to the target as compared to parent epitope.
Multi-User Channel Estimation Exploiting Pulse Shaping Information (1998)

Publication in the conference proceedings of EUSIPCO, Rhodes, Greece, 1998
Presence of an antigenic determinant common to rat IgE-potentiating factor, IgE-suppressive factor, and Fc epsilon receptors on T and B lymphocytes. (1984)

Polyclonal antibodies against purified IgE-potentiating factor were prepared in guinea pigs, and mouse monoclonal antibodies were prepared against inactive IgE-binding factor from a T cell hybridoma. The polyclonal antibodies and two of the monoclonal antibodies bound the IgE-potentiating factor, the IgE suppressive factor, and the inactive IgE-binding factor. The results indicate that the three IgE-binding factor molecules share a common antigenic determinant. The polyclonal antibodies and the monoclonal antibody bound intracellular IgE-binding factors that did not have affinity for either lentil lectin or peanut agglutinin, which suggests that the antibodies were directed against the peptide portion of IgE-binding factors. Pretreatment of Fc epsilon R+ T hybridoma cells and Fc epsilon R+ B cells with either the monoclonal or the polyclonal anti-IgE-binding factor (anti-IgE-bF) antibody prevented rosette formation of the cells with IgE-coated erythrocytes, whereas the same treatment failed to affect rosette formation of Fc gamma R+ cells with IgG-coated erythrocytes. Specific binding of the guinea pig anti-IgE-bF antibodies to Fc epsilon R on both B and T cells was confirmed by immunofluorescence. The results indicate that Fc epsilon R on B and T cells share a common antigenic determinant with IgE-binding factors. The F(ab')2 fragments of the guinea pig anti-IgE-bF induced the expression of Fc epsilon R on Fc gamma R+ lymphocytes and the formation of IgE-binding factors. The capacities of not only IgE, but also anti-IgE-bF, to induce both Fc epsilon R expression and IgE-binding factor formation indicate that Fc epsilon R on lymphocytes, rather than IgE, transmit the signal for the formation of IgE-binding molecules.
Power systems marginal cost curve and its applications (1995)

This paper presents a forward recursive procedure to calculate the expected system marginal cost curve (EMC). The EMC formulation allows for multi-state and multi-block dispatch of generating units and is used to determine the optimal energy of pumped-storage units. A new approach is developed to compute the first and second derivatives of the expected generation energy of a thermal unit with respect to the capacity of all thermal units in the system. The salient feature of the proposed approach is that it applies to hydro-thermal systems with multiple limited-energy hydro units.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Some Hydraulic and Wicking Properties of St. Cloud Zeolite and Zeolite-Soil Mixtures (2011)

In many riparian regions of New Mexico, indigenous vegetation has been replaced by invasive plant species such as saltcedar (Tamarix spp.) and Russian olive (Elaeagnus angustifolia). The management of these species has been costly, and re-establishment of indigenous vegetation to improve biodiversity has not been successful, especially due to the lack of precipitation water available for new plant growth. New Mexico has a dry, hot climate with a mean annual precipitation of 230 mm in the riparian regions. This study was conducted to determine the possible use of clinoptilolite zeolite (CZ) as a wicking material to raise a sufficient amount of water within the vadose zone from the underlying water table for plant growth. Twelve different core samples were repacked with five different sized CZs, three different soils, three CZ-soil mixtures, and one clay-sand mixture. They were used to determine saturated hydraulic conductivities (Ks) and soil water characteristic curves (SWCC). The RETC program was used to fit the empirical Brooks and Corey (BC) and van Genuchten (VG) models to the measured SWCC. The Ks ranged from 4.27 10-5 to 4.42 10-1 cm/s for CZ, 8.32 10-5 to 2.40 10-3 cm/s for field soils, and 1.26 10-4 to 4.43 10-4 cm/s for soil mixtures. The available water content (AWC), assessed as the difference between the volumetric soil moisture contents at -0.3 and -15 bars, was greatest for fine CZ (25.4%) and lowest for medium CZ (2.5%). The Ks of clay (8.32 10-5 cm/s) was consistently lower than for a mixture of clay and fine-medium CZ (1.26 10-4 cm/s). The Ks of sandy loam and alluvial sand decreased from 8.56 10-4 cm/s to 3.56 10-4 cm/s and from 2.40 10-3 cm/s to 4.43 10-4 cm/s, respectively, when mixed with fine-medium CZ. The AWC was reduced from 19% to about 10% when fine-medium CZ was mixed with clay. Predicted capillary rise in fine CZ using the Lu and Likos (2004) model with a values obtained from BC retention function was 299.5 cm whereas the measured capillary rise in the repacked laboratory column with CZ was 317 cm for 360 days. However, predicted and measured capillary rise reached 150 cm within 22 days. Mixing of fine-medium CZ with sand produced a 33% increase in the predicted capillary rise within 1.5 days. Mixing of clay with sand increased the predicted capillary rise by 336% by the end of 16 days. Since Ks and AWC of the CZ-sand mix and clay-sand mix did not differ significantly, both CZ and clay could be used as wicking materials. It would be easier to use CZ because it is available commercially and sand-zeolite mixture would be more practical. The results demonstrate the potential of CZ to be used as a material for improving the hydraulic and wicking properties of sand in riparian regions.
MTORC2 activity disrupts lysosome acidification in systemic lupus erythematosus by impairing caspase-1 cleavage of Rab39a (2020)

Lysosomes maintain immune homeostasis through the degradation of phagocytosed apoptotic debris; however, the signaling events regulating lysosomal maturation remain undefined. In this study, we show that lysosome acidification, key to the maturation process, relies on mTOR complex 2 (mTORC2), activation of caspase-1, and cleavage of Rab39a. Mechanistically, the localization of cofilin to the phagosome recruits caspase-11, which results in the localized activation of caspase-1. Caspase-1 subsequently cleaves Rab39a on the phagosomal membrane, promoting lysosome acidification. Although caspase-1 is critical for lysosome acidification, its activation is independent of inflammasomes and cell death mediated by apoptosis-associated speck-like protein containing a caspase recruitment domain, revealing a role beyond pyroptosis. In lupus-prone murine macrophages, chronic mTORC2 activity decouples the signaling pathway, leaving Rab39a intact. As a result, the lysosome does not acidify, and degradation is impaired, thereby heightening the burden of immune complexes that activate FcgRI and sustain mTORC2 activity. This feedforward loop promotes chronic immune activation, leading to multiple lupus-associated pathologies. In summary, these findings identify the key molecules in a previously unappreciated signaling pathway that promote lysosome acidification. It also shows that this pathway is disrupted in systemic lupus erythematosus.
A methodology for building a fault diagnoser for hybrid systems (2011)

In this paper, a design methodology for building diagnosers for hybrid systems
is proposed. The design methodology uses as a starting point a hybrid automaton model to
represent the hybrid system behaviour by means of the interaction of continuous dynamics and discrete events. Then, a hybrid fault diagnoser is designed using the methodology described in this paper and implemented by means of a discrete event system which carries out the mode recognition and diagnostic tasks, both based on residuals generated using models. Both tasks interact each other since the diagnosis module adapts according to the current mode of the hybrid system. The mode recognition task involves detecting and identifying the mode change by determining the set of residuals that are consistent with the current mode of the hybrid system.
On the other hand, the diagnostic task involves detecting and isolating faults by identifying the fault that can explain the set of residuals that are inconsistent. A section of the Barcelona sewer network is used as application case study to illustrate the proposed fault diagnosis for hybrid
systems.