gebhart/patrepeval huggingface dataset:
Analysis of the CDR3 region of the rearranged IgH chain genes in patients with severe combined immunodeficiency and severe lymphopenia (1996)

Human B cell-negative severe combined immunodeficiency (B-SCID) is a primary immunodeficiency disease characterized by both T and B lymphocytopenia and agammaglobulinemia. Although lymphocytes of B-SCID patients express defective recombinase activity and rarely succeed in making Ag receptors, the molecular defect of the human B-SCID remains to be identified. To gain more insight into the human B-SCID defect and its effect on the Ab repertoire, we examined the Ig heavy (H) chain genes of the peripheral blood leaky B cells from three B-SCID patients. Although the number of B cells in their peripheral blood was very limited, we could obtain 41 productive VDJ recombinations from the 58 joints. The recombinations showed a grossly altered pattern characterized by short N nucleotides, short deleted nucleotides from 5' JH segments, immature JH and D segment utilization, absence of VDDJ recombination, and all but one JH segment equal to germline JH segments. Therefore, Ab repertoire of IgH chain gene in human B-SCID was limited because of restricted junctional and combinatorial diversity and few somatic mutations. Furthermore, unusually long P nucleotides were inserted in junctional sequences, which might indicate that resolution of hairpin is impaired in human B-SCID as in the murine SCID.
Elevation of Hippocampal Neurogenesis Induces a Temporally Graded Pattern of Forgetting of Contextual Fear Memories (2018)

Throughout life neurons are continuously generated in the subgranular zone of the hippocampus. The subsequent integration of newly generated neurons alters patterns of dentate gyrus input and output connectivity, potentially rendering memories already stored in those circuits harder to access. Consistent with this prediction, we previously showed that increasing hippocampal neurogenesis after training induces forgetting of hippocampus-dependent memories, including contextual fear memory. However, the brain regions supporting contextual fear memories change with time, and this time-dependent memory reorganization might regulate the sensitivity of contextual fear memories to fluctuations in hippocampal neurogenesis. By virally expressing the inhibitory designer receptor exclusively activated by designer drugs, hM4Di, we first confirmed that chemogenetic inhibition of dorsal hippocampal neurons impairs retrieval of recent (day-old) but not remote (month-old) contextual fear memories in male mice. We then contrasted the effects of increasing hippocampal neurogenesis at recent versus remote time points after contextual fear conditioning in male and female mice. Increasing hippocampal neurogenesis immediately following training reduced conditioned freezing when mice were replaced in the context 1 month later. In contrast, when hippocampal neurogenesis was increased time points remote to training, conditioned freezing levels were unaltered when mice were subsequently tested. These temporally graded forgetting effects were observed using both environmental and genetic interventions to increase hippocampal neurogenesis. Our experiments identify memory age as a boundary condition for neurogenesis-mediated forgetting and suggest that, as contextual fear memories mature, they become less sensitive to changes in hippocampal neurogenesis levels because they no longer depend on the hippocampus for their expression.<b>SIGNIFICANCE STATEMENT</b> New neurons are generated in the hippocampus throughout life. As they integrate into the hippocampus, they remodel neural circuitry, potentially making information stored in those circuits harder to access. Consistent with this, increasing hippocampal neurogenesis after learning induces forgetting of the learnt information. The current study in mice asks whether these forgetting effects depend on the age of the memory. We found that post-training increases in hippocampal neurogenesis only impacted recently acquired, and not remotely acquired, hippocampal memories. These experiments identify memory age as a boundary condition for neurogenesis-mediated forgetting, and suggest remote memories are less sensitive to changes in hippocampal neurogenesis levels because they no longer depend critically on the hippocampus for their expression.
[Repair of damage caused by 313 nm light and photoprotection in Candida guilliermondii]. (1977)

The study of the effect of near-UV light (300-380 nm) on the yeast Candida guilliermondii has shown that certain doses of 313 nm light cause inactivation which is reversible after the cells have been kept for some time in a non-nutrient medium. The findings suggest a different nature of the lesions resulting in killing the cells irradiated with light of 313 and 254 nm. The data obtained are interpreted in terms of a new, yet unknown, repair mechanism, other than the classical dark reparation, which is involved in the recovery of cells inactivated by light of 313 nm. Non-lethal doses at 313 nm induce photoprotection of the cells against UV lesions. The effect was compared with the photoprotection described in literature, and was found to be different.
Cloning and Sequence Analyses of cDNAs Encoding Aminoacylase I from Porcine Kidney (1992)

cDNAs encoding L-aminoacylase (EC 3.5.1.14) were isolated from a lambda gt10 cDNA library derived from porcine kidney mRNA. The clones were identified by hybridization with a synthetic oligonucleotide probe based on partial peptide sequences, or with a DNA probe encoding human aminoacylase I. Several cDNA clones isolated from the library had a length of about 1.3 kbp. They contained an open reading frame of 1218 bp encoding a polypeptide of 406 amino acids. The deduced amino-acid sequence contains the known peptide sequences; in addition, M(r) (45.3 kDa) and amino-acid composition of the predicted polypeptide match those of purified aminoacylase I. Data base searches did not reveal significant sequence homologies of aminoacylase I with other well-known amidases.
Enhancement of data retention time in DRAM using step gated asymmetric(STAR) cell transistors (2005)

For the first time, we developed successfully the 512Mb DRAMs using step-gated-asymmetric (STAR) cell transistors with 90nm feature size. The STAR with step recessed channel depth of 40nm exhibits distinctly improved electrical characteristics such as BV/sub DS/, junction leakage and word-line capacitance (C/sub WL/), comparing to a conventional planar and recess-channel transistors of the same gate length. The two major merits using the STAR in DRAMs are about 200% improvement of data retention time and low costs of KrF lithography process rather than those of ArF lithography process. Moreover, this STAR technology is able to extend to sub-80nm by scaling STAR depth and width without increasing the concentration of substrate.
Structural Underpinnings of the Enhanced Cycling Stability upon Al-Substitution in LiNi<sub>0.45</sub>Mn<sub>0.45</sub>Co<sub>0.1–<i>y</i></sub>Al<sub><i>y</i></sub>O<sub>2</sub> Positive Electrode Materials for Li-ion Batteries (2012)

Single-phase LiNi0.45Mn0.45Co0.1–yAlyO2 layered oxide materials with 0 ≤ y ≤ 0.10 were prepared using the glycine-nitrate combustion method. Al-substitution has a minimal effect on the defect concentration and rate capability of the materials, but raises the operating voltage and reduces the capacity fade of the materials during prolonged cycling compared to the unsubstituted system. In situ X-ray diffraction suggests the presence of Al has a significant structural impact during battery operation. It acts to limit the changes in lattice parameters observed during electrochemical charging and cycling of the materials. High-resolution X-ray diffraction reveals structural distortions in the transition metal layers of as-synthesized powders with high Al-contents, as well as a structural evolution seen in all materials after cycling.
A Multivariate Discretization Method for Learning Bayesian Networks from Mixed Data (2013)

In this paper we address the problem of discretization in the context of learning Bayesian networks (BNs) from data containing both continuous and discrete variables. We describe a new technique for multivariate discretization, whereby each continuous variable is discretized while taking into account its interaction with the other variables. The technique is based on the use of a Bayesian scoring metric that scores the discretization policy for a continuous variable given a BN structure and the observed data. Since the metric is relative to the BN structure currently being evaluated, the discretization of a variable needs to be dynamically adjusted as the BN structure changes.
Sugarcane Borer (Lepidoptera: Crambidae) Management Threshold Assessment on Four Sugarcane Cultivars (2006)

This research assesses the potential for using different economic injury thresholds in management of a key insect pest on susceptible and resistant commercially produced cultivars of sugarcane (Saccharum spp. hybrids). In a 2-yr sugarcane borer, Diatraea saccharalis (F.) (Lepidoptera: Crambidae), study involving four commercially produced sugarcane cultivars and four insecticide treatment thresholds, ‘LCP 85-384’ and ‘HoCP 91-555’ were the most susceptible based on percentage of bored internodes compared with the more resistant ‘HoCP 85-845’ and ‘CP 70-321’. In 2001, the 10% infested stalks threshold was not as effective as the 5% early season-10% late season and 5% full season for HoCP 91-555. Based on D. saccharalis injury under natural infestation conditions, susceptible cultivars seem to require a lower infestation threshold than the more resistant cultivars to achieve adequate injury reduction. Among yield components, only the theoretical recoverable sugar per stalk was significantly increased by applying insecticides. With the resistant HoCP 85-845, differences were not detected for percentage of bored internodes among treated versus untreated management regimes. The resistant HoCP 85-845 had higher levels of fiber in our study; however, no clear pattern on resistance mechanisms was established, because the resistant cultivar CP 70-321 had comparatively low levels of fiber. The development of cultivar-specific thresholds is expected to lower the amount of insecticide used for D. saccharalis management in the sugarcane industry, reduce selection pressure, and delay the development of insecticide resistance.
Urinary 2‐ethyl‐3‐oxohexanoic acid as major metabolite of orally administered 2‐ethylhexanoic acid in human (2007)

Human metabolism of 2-ethylhexanoic acid (2-EHA), which is a known metabolite of important phthalates, was investigated using 2-EHA-contaminated food. The results of our studies reveal that the major catabolic pathway of 2-EHA in human is beta-oxidation. The dominant final urinary metabolite was identified and quantified as 3-oxo-2-ethylhexanoic acid (3-oxo-2-EHA), but only after immediate methylation of the extract from urine and prior to GC-MS analysis. Former studies without the precaution of immediate methylation had found 4-heptanone as the major metabolite, which is obviously an artifact arising from the decarboxylation of 3-oxo-2-EHA.
Pose-Invariant Face Alignment with a Single CNN (2017)

Face alignment has witnessed substantial progress in the last decade. One of the recent focuses has been aligning a dense 3D face shape to face images with large head poses. The dominant technology used is based on the cascade of regressors, e.g., CNN, which has shown promising results. Nonetheless, the cascade of CNNs suffers from several drawbacks, e.g., lack of end-to-end training, hand-crafted features and slow training speed. To address these issues, we propose a new layer, named visualization layer, that can be integrated into the CNN architecture and enables joint optimization with different loss functions. Extensive evaluation of the proposed method on multiple datasets demonstrates state-of-the-art accuracy, while reducing the training time by more than half compared to the typical cascade of CNNs. In addition, we compare multiple CNN architectures with the visualization layer to further demonstrate the advantage of its utilization.
Ca2+ exchange with troponin C and cardiac muscle dynamics (2007)

Controversy abounds in the cardiac muscle literature over the rate-limiting steps of cardiac muscle contraction and relaxation. However, the idea of a single biochemical mechanism being the all-inclusive rate-limiting step for cardiac muscle contraction and relaxation may be oversimplified. There is ample evidence that Ca(2+) concentration and dynamics, intrinsic cross-bridge properties, and even troponin C (TnC) Ca(2+) binding and dissociation can all modulate the mechanical events of cardiac muscle contraction and relaxation. However, TnC has generally been thought to play no role in influencing cardiac muscle dynamics due to the idea that Ca(2+) exchange with TnC is very rapid. This definitely is the case for isolated TnC, but not for the more sophisticated biochemical systems of reconstituted thin filaments and myofibrils. This review will discuss the biochemical influences on Ca(2+) exchange with TnC and their physiological implications.
The Impact of an Improvised Social Work Method in a School: Aspirations, Encouragement, Realism and Openness (2010)

A high school in the English West Midlands reduces annual school exclusions from 251 to 6 in three years. A social worker is employed by the school to join the student support services. A new method of brief intervention is introduced by the social worker based on 'aspirations, encouragement, realism and openness' (AERO), summarised by one teacher as helping a conversation develop in which the young people can discuss problems that they would otherwise find difficult. All of this is established with no special pilot project status or resources. This article considers the relationship between these factors and evaluates the impact of the AERO method through interviews with key participants — 12 students currently in school and one parent, all of whom had direct experience of the method, and six professionals who experienced the impact of the model. The findings suggest that the philosophy of social inclusion introduced by a new head teacher is sustained by a systematic approach to providing social and personal support to students, and by the use of an effective and efficient practice method. The article discusses the possibilities of transferring the lessons from this study and also the possible limitations of the social work method and the study itself.
The human natural killer cytotoxic cell line NK-92, once armed with a murine CD16 receptor, represents a convenient cellular tool for the screening of mouse mAbs according to their ADCC potential (2013)

To take advantage of the large number of well-characterized mouse immunoglobulins (IgGs) for the study of antibody-dependent cell-mediated cytotoxicity (ADCC) in human cells, we armed human cytotoxic lymphocytes with a mouse receptor for the Fc portion of IgG antibodies. The human ΝΚ-92 natural killer cell line was transduced with a mouse receptor gene (mCD16), which was stably expressed on the cell surface (referred to as NK-92 (mCD16) ). When tested against a B-lymphoblastoid cell line (BLCL) coated with mouse anti-CD20 IgG1, IgG2a or IgG2b monoclonal antibodies (mAbs), the newly expressed mouse Fc receptor enabled the NK-92 (mCD16) cells to kill the BLCL by ADCC. Next, using the NK-92 (mCD16) we compared mouse mAbs directed at B lineage specific CD antigens for their ability to induce ADCC against human Epstein-Barr virus- infected B lymphoblastoid (for anti-CD19, -CD20 and -CD21) or against myeloma (for anti-CD38 and -CD138) target cells. Our results demonstrated that the "NK-92 (mCD16) assay" allows convenient and sensitive discrimination of mouse mAbs for their ability to mediate ADCC in a human cellular system. In addition, our results provide examples of dissociation between opsonization and target cell killing through ADCC. These "murinized" human effector cells thus represent a convenient cellular tool for the study of ADCC.
Neonatal outcome in a Danish national cohort of 8602 children born after in vitro fertilization or intracytoplasmic sperm injection: the role of twin pregnancy (2004)

Background. In Denmark, 4% of all infants are born after in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI) and 40% of these children are twins. Methods. We investigated neonatal outcome in a complete Danish IVF/ICSI birth cohort including 8602 infants born between 1995 and 2000: 3438 twins (40%) and 5164 singletons (60%). Births conceived after IVF or ICSI were identified by record linkage with the Danish IVF Registry and the National Medical Birth Registry. Data on neonatal outcome were collected from the National Patient Registry. Results. IVF/ICSI twins had a 10-fold increased age- and parity-adjusted risk of delivery before 37 completed weeks [odds ratio (OR) 9.9, 95% confidence interval (95% CI) 8.7–11.3] and a 7.4-fold increased risk of delivery before 32 completed weeks (OR 7.4, 95% CI 5.6–9.8) compared with singletons. Correspondingly, ORs of birthweight <2500 g and birthweight <1500 g in twins were 11.8 (95% CI 10.3–13.6) and 5.4 (95% CI 4.1–7.0), respectively. The stillbirth rate was doubled in twins (13.1/1000) compared with singletons (6.6/1000) (p = 0.002). The risk of cesarean section and of admittance to a neonatal intensive care unit (NICU) was 4.6- and 1.8-fold higher in IVF/ICSI twins than in singletons. The rate of major malformations was 40.4/1000 in twins and 36.8/1000 in singletons (p = 0.4), whereas the total malformation rate (major + minor) was higher in twins (73.7/1000) than in singletons (55.0/1000) (p = 0.001). After exclusion of patent ductus arteriosus (PDA), which is strongly associated with preterm birth, no significant differences in any malformation rates were observed between twins and singletons. Apart from the frequency of ICSI children with hypospadias, which reached a significance level of p = 0.05, malformation rates in ICSI children were similar to those in IVF children. Conclusions. This study indicates that neonatal outcome in IVF/ICSI twins is considerably poorer than in singletons. Thus, the impact is to draw the attention of clinicians to the benefit of elective single embryo transfer (eSET).
Circulating Dipeptidyl Peptidase 3 and Alteration in Haemodynamics in Cardiogenic Shock: Results from the OptimaCC Trial (2019)

clinicaltrials.gov Identifier NCT01367743.
Transductional evidence for plasmid linkage of lactose metabolism in streptococcus lactis C2 (1976)

A lactose-negative (Lac-), proteinase-negative (Prt-) mutant, designated C145 was isolated from Streptococcus lactis C2 after treatment with nitrosoguanidine and ultraviolet irradiation. The mutant appeared to be cured of the prophage(s) present in S. lactis C2 based on non-inducibility by ultraviolet irradiation or mitomycin C. When cleared lysate material from C145 was subjected, to cesium chloride-ethidum bromide (EB) density gradient centrifugation, no plasmid peak was observed, suggesting that C145 was cured of plasmid deoxyribonucleic and (DNA). A histogram showing distribution of contour lengths of circular molecules of DNA from C145, however, revealed the presence of a greatly diminished number of DNA molecules as compared with the parent culture and indicated the absence of the 30 x 10(6) plasmid. Cesium chloride-ethidium bromide gradient profiles from Lac+, Prt- and Lac+ Prt+ transductants of C145 revealed no plasmid peak, but electron microscopy of the fractions normally possessing the satellite band of DNA showed the presence of a new plasmid species having a molecular weight from 20 x 10(6) to 22 x 10(6). This plasmid was lost when the transductants became Lac-. Examination of a plasmid histogram from a spontaneous Lac- Prt- mutants of S. lactis C2 resembled that of C145, with the absence of the 30 x 10(6) plasmid and the presence of the 22 x 10(6) plasmid in Lac+ Prt+ transductants. The results suggest that lactose metabolism is mediated through the 30 x 10(6) plasmid in S. lactis C2 and that the transducing bacteriophage, which is too small to accommodate the entire plasmid, is transferring about two-thirds of the original plasmid through a process termed transductional shortening.
[Medicinal Lamiaceae with antioxidant properties, a potential source of rosmarinic acid]. (1991)

Hydroalcholic extracts from four native medicinal Lamiaceae, Lycopus europaeus L., Melissa officinalis L., Origanum vulgare L. and Prunella vulgaris L. have shown significant antioxidative activities, by free radical scavenger effect on DPPH, compared with those of Rosmarinus officinalis L. and Salvia officinalis L. extracts. The antioxidative activity was partly in relation to the rosmarinic acid content. The major hydroxycinnamic compound, quantitatively determinated by HPLC, was present in large amount. The content in Prunella vulgaris L. spikes average 6.1%, based on dry weight.
Frequency‐domain modelling of airborne electromagnetic responses using staggered finite differences<sup>1</sup> (1995)

Abstract A 3D frequency‐domain EM modelling code has been implemented for helicopter electromagnetic (HEM) simulations. A vector Helmholtz equation for the electric fields is employed to avoid convergence problems associated with the first‐order Maxwell's equations when air is present. Additional stability is introduced by formulating the problem in terms of the scattered electric fields. With this formulation the impressed dipole source is replaced with an equivalent source, which for the airborne configuration possesses a smoother spatial dependence and is easier to model. In order to compute this equivalent source, a primary field arising from dipole sources of either a whole space or a layered half‐space must be calculated at locations where the conductivity is different from that of the background. The Helmholtz equation is approximated using finite differences on a staggered grid. After finite‐differencing, a complex‐symmetric matrix system of equations is assembled and preconditioned using Jacobi scaling before it is solved using the quasi‐minimum residual (QMR) method. The modelling code has been compared with other 1D and 3D numerical models and is found to produce results in good agreement. We have used the solution to simulate novel HEM responses that are computationally intractable using integral equation (IE) solutions. These simulations include a 2D conductor residing at a fault contact with and without topography. Our simulations show that the quadrature response is a very good indicator of the faulted background, while the in‐phase response indicates the presence of the conductor. However when interpreting the in‐phase response, it is possible erroneously to infer a dipping conductor due to the contribution of the faulted background.
INTERACTIVE SURFACE ADJUSTMENT OF MARINE PROPELLERS (1978)

A generalized interactive method is presented for the adjustment of any selected subregions on a propeller before its manufacture by an NC (numerically controlled) machining process. The adjustment computer program is flexible and can produce a smooth approximately slope-continuous surface. The adjustment is made by first rectifying, normalizing and transforming the defined subregion into a unit circle in the plane view. If this region is then regarded as the plan view of a thin, plane elastic plate, the shape of the plate when displaced laterally at any selected point can be computed by Foeppl's or Michell's solution for such a case. This influence surface may then be superimposed on the shape of the original (transformed within the unit circle) to change its shape. The process is iterative and retentive of all data; it may be monitored on a computer graphics terminal while successive modifications proceed under full control towards a desired form of the propeller blade or hub surface.