gebhart/patrepeval huggingface dataset:
Legal Judgment Prediction via Topological Learning (2018)

Legal Judgment Prediction (LJP) aims to predict the judgment result based on the facts of a case and becomes a promising application of artificial intelligence techniques in the legal field. In real-world scenarios, legal judgment usually consists of multiple subtasks, such as the decisions of applicable law articles, charges, fines, and the term of penalty. Moreover, there exist topological dependencies among these subtasks. While most existing works only focus on a specific subtask of judgment prediction and ignore the dependencies among subtasks, we formalize the dependencies among subtasks as a Directed Acyclic Graph (DAG) and propose a topological multi-task learning framework, TOP-JUDGE, which incorporates multiple subtasks and DAG dependencies into judgment prediction. We conduct experiments on several realworld large-scale datasets of criminal cases in the civil law system. Experimental results show that our model achieves consistent and significant improvements over baselines on all judgment prediction tasks. The source code can be obtained from https://github. com/thunlp/TopJudge.
A mass spectrometric “Western blot” to evaluate the correlations between histone methylation and histone acetylation (2004)

Histone acetylation, methylation, and phosphorylation occur predominantly in the unstructured N-terminal domains or histone "tails". These modifications and others comprise a "histone code" that directly facilitates or antagonizes association of regulatory proteins with nucleosomes to mediate changes in chromatin structure and activity. Methylation of histone H3 outside of the tail region at lysine 79 has been reported for a variety of species ranging from yeast to humans and in some gene-specific cases appears to be associated with active chromatin and transcription. Whether methylation of lysine 79 is associated with other post-translational modifications of the H3 tail is unknown. Using mass spectrometric relative quantitation, a mass spectrometric "Western blot", we compare methylation at lysines 4, 9, and 79 with acetylation of human histone H3. We find that the total levels of lysine 4 and 79 methylation (combined mono-, di-, and trimethylation) in the H3 population increase with the degree of H3 tail acetylation. The total amount of lysine 4 methylation increases progressively from less than 10% in the nonacetylated H3 to greater than 90% in the penta-acetylated H3. In addition, significant levels of lysine 4 trimethylation also occur in combination with the penta-acetylated H3 species. In contrast, the level of H3 lysine 9 trimethylation is greatest for the monoacetylated species while H3 lysine 9 acetylation occurs predominantly in hyperacetylated (tetra- and penta-acetylated) H3 isoforms. Together, these results indicate that methylation of lysine 4 and 79 as well as the switch from lysine 9 methylation to acetylation are coordinated synchronously with H3 hyperacetylation as marks of active chromatin.
Scalable replay-based replication for fast databases (2017)

Primary-backup replication is commonly used for providing fault tolerance in databases. It is performed by replaying the database recovery log on a backup server. Such a scheme raises several challenges for modern, high-throughput multi-core databases. It is hard to replay the recovery log concurrently, and so the backup can become the bottleneck. Moreover, with the high transaction rates on the primary, the log transfer can cause network bottlenecks. Both these bottlenecks can significantly slow the primary database. In this paper, we propose using record-replay for replicating fast databases. Our design enables replay to be performed scalably and concurrently, so that the backup performance scales with the primary performance. At the same time, our approach requires only 15--20% of the network bandwidth required by traditional logging, reducing network infrastructure costs significantly.
Immunization of Rhesus Macaques with a DNA Prime/Modified Vaccinia Virus Ankara Boost Regimen Induces Broad Simian Immunodeficiency Virus (SIV)-Specific T-Cell Responses and Reduces Initial Viral Replication but Does Not Prevent Disease Progression following Challenge with Pathogenic SIVmac239 (2002)

Producing a prophylactic vaccine for human immunodeficiency virus (HIV) has proven to be a challenge. Most biological isolates of HIV are difficult to neutralize, so that conventional subunit-based antibody-inducing vaccines are unlikely to be very effective. In the rhesus macaque model, some protection was afforded by DNA/recombinant viral vector vaccines. However, these studies used as the challenge virus SHIV-89.6P, which is neutralizable, making it difficult to determine whether the observed protection was due to cellular immunity, humoral immunity, or a combination of both. In this study, we used a DNA prime/modified vaccinia virus Ankara boost regimen to immunize rhesus macaques against nearly all simian immunodeficiency virus (SIV) proteins. These animals were challenged intrarectally with pathogenic molecularly cloned SIVmac239, which is resistant to neutralization. The immunization regimen resulted in the induction of virus-specific CD8(+) and CD4(+) responses in all vaccinees. Although anamnestic neutralizing antibody responses against laboratory-adapted SIVmac251 developed after the challenge, no neutralizing antibodies against SIVmac239 were detectable. Vaccinated animals had significantly reduced peak viremia compared with controls (P < 0.01). However, despite the induction of virus-specific cellular immune responses and reduced peak viral loads, most animals still suffered from gradual CD4 depletion and progressed to disease.
X-ray digital linear tomosynthesis imaging (2011)

Aims: The purpose of this review includes the fol-lowing: 1) to identify indications for volumetric X-ray digital linear tomosynthesis by using a filtered back projection (FBP) algorithm and 2) to compare X-ray digital linear tomosynthesis, X-ray digital ra-diography, conventional tomography, and computed tomography. Review: The methods include the fol-lowing: 1) an overview of the tomosynthesis system in comparison with conventional X-ray imaging tech-nology; 2) an overview of the properties of diagnostic imaging for the chest, hip joint, and temporomandibular joint when imaging overlying structures and their effect of various artificial images; and 3) a review of each system. Summary: Tomosynthesis is worthy of further evaluation because of its flexibility and ability to suppress streak artifacts through an appropriate choice of an FBP algorithm. Tomosynthesis may be considered the imaging technique of choice for investigation of bone changes and detection of pulmonary nodules. Understanding the potential of tomosynthesis imaging will improve diagnostic accuracy in clinical applications.
Identification of Piwil2-Like (PL2L) Proteins that Promote Tumorigenesis (2010)

PIWIL2, a member of PIWI/AGO gene family, is expressed in the germline stem cells (GSCs) of testis for gametogenesis but not in adult somatic and stem cells. It has been implicated to play an important role in tumor development. We have previously reported that precancerous stem cells (pCSCs) constitutively express Piwil2 transcripts to promote their proliferation. Here we show that these transcripts de facto represent Piwil2-like (PL2L) proteins. We have identified several PL2L proteins including PL2L80, PL2L60, PL2L50 and PL2L40, using combined methods of Gene-Exon-Mapping Reverse Transcription Polymerase Chain Reaction (GEM RT-PCR), bioinformatics and a group of novel monoclonal antibodies. Among them, PL2L60 rather than Piwil2 and other PL2L proteins is predominantly expressed in various types of human and mouse tumor cells. It promotes tumor cell survival and proliferation in vitro through up-regulation of Stat3 and Bcl2 gene expressions, the cell cycle entry from G(0/1) into S-phase, and the nuclear expression of NF-κB, which contribute to the tumorigenicity of tumor cells in vivo. Consistently, PL2L proteins rather than Piwil2 are predominantly expressed in the cytoplasm or cytoplasm and nucleus of euchromatin-enriched tumor cells in human primary and metastatic cancers, such as breast and cervical cancers. Moreover, nuclear PL2L proteins are always co-expressed with nuclear NF-κB. These results reveal that PL2L60 can coordinate with NF-κB to promote tumorigenesis and might mediate a common pathway for tumor development without tissue restriction. The identification of PL2L proteins provides a novel insight into the mechanisms of cancer development as well as a novel bridge linking cancer diagnostics and anticancer drug development.
Strategies for the Isolation and Characterization of Antimicrobial Peptides of Invertebrates (2003)

Resistance of bacteria to antibiotics has become one of the main problems in human health. In addition, in agronomy, microbial diseases are largely responsible for the decrease in agricultural production. The discovery of new antibiotic families is a way to circumvent such problems and antimicrobial peptides may represent a new type of such antibiotics.
PSEUDOCOLOR AS A MEANS OF IMAGE ENHANCEMENT (1969)

For human observers the number of distinguishably different colors is much larger than the number of distinguishably different shades of gray. Therefore, if the scale of grays in a complex black-and-white image, such as an X-ray, is transformed into some suitable scale of colors, perception of the details in that image will be greatly enhanced. In one versatile but expensive method of producing such pseudocolor images, the black-and-white image is photoelectrically scanned and a computer is used to produce three pseudocolor separation positives (or negatives) directly on 35 mm film. A simpler and inexpensive method has been developed which uses purely photographic procedures. Examples of results with this procedure applied to chromosome photomicrographs, X-ray films, and pathological specimens are presented.
<title>Active vibration isolation on an experimental flexible structure</title> (1993)

The paper describes experimental research in the area of active vibration isolation. The objective of the research is to quantitatively assess the performance gained by augmenting a passive isolator with an active stage. Vibration isolation experiments were carried out on a flexible structure utilizing a proof-mass shaker as the disturbance source and a newly developed active member as the isolator. Broad band force feedback control demonstrated more than 20 dB reduction in force transmissibility over passive isolation alone. The broad band controller was augmented with notch filters which resulted in reducing force transmissibility by 40 dB over the passive stage in select narrow bands.
Modified method for determining carcinoembryonic antigen in the presence of human anti-murine antibodies (1993)

Abstract The increasing use of monoclonal antibodies (MAbs) for disease diagnosis and therapy has created a class of patients at risk for systematic error in clinical testing due to interference by human anti-murine antibodies (HAMA). HAMA interference is often difficult to detect and can cause either an increase or a decrease in apparent concentrations of antigen present. We undertook a clinical study to test a HAMA-resistant enzyme immunoassay (EIA) format for carcinoembryonic antigen (CEA) determination. Using the Food and Drug Administration-approved CEA-EIA Monoclonal One-Step Assay (Abbott) with the addition of an acid/heat extraction of patients' specimens, we found that the resulting CEA values accurately reflected the patients' status. We demonstrated that the acid/heat-extracted specimens yield linear dilution curves and show analytical recoveries of added CEA in the range of 76-123% in HAMA-positive specimens and 86-103% in HAMA-negative specimens. The correlation of CEA values in extracted vs unextracted specimens from 184 patients and control subjects was 0.9963. The CEA detection limit of the assay was 1.6 micrograms/L for the extracted samples.
Thermal avoidance in <i>Caenorhabditis elegans</i> : An approach to the study of nociception (1999)

Upon perception of a noxious stimulus, an organism executes defense mechanisms, such as escape responses. The molecular basis of these mechanisms is poorly understood. In this paper we show that upon exposure to noxious temperature, Caenorhabditis elegans reacts by a withdrawal reflex. To analyze this thermal avoidance behavior, we developed a laser-based assay to quantify the response. The escape reflex can be observed in 98% of the adult animals, but is not executed in animals in diapause. The thermal avoidance response differs significantly from the thermotaxis behavior that is based on the perception of physiological temperature. It involves different neurons and is influenced by mutations in distinct genes. As in mammals, the strength of the thermal avoidance response is increased by application of capsaicin, the pungent ingredient in chili peppers. We find that thermal avoidance is strongly reduced in mutants affecting the neural transmission modulated by glutamate and neuropeptides as well as in mutants affecting the structure and function of sensory neurons. We suggest that the study of this nociceptive behavior in C. elegans can be used to understand the genetic and molecular basis of thermal nociception.
Atmospheric Turbulence Mitigation Using Complex Wavelet-Based Fusion (2013)

Restoring a scene distorted by atmospheric turbulence is a challenging problem in video surveillance. The effect, caused by random, spatially varying, perturbations, makes a model-based solution difficult and in most cases, impractical. In this paper, we propose a novel method for mitigating the effects of atmospheric distortion on observed images, particularly airborne turbulence which can severely degrade a region of interest (ROI). In order to extract accurate detail about objects behind the distorting layer, a simple and efficient frame selection method is proposed to select informative ROIs only from good-quality frames. The ROIs in each frame are then registered to further reduce offsets and distortions. We solve the space-varying distortion problem using region-level fusion based on the dual tree complex wavelet transform. Finally, contrast enhancement is applied. We further propose a learning-based metric specifically for image quality assessment in the presence of atmospheric distortion. This is capable of estimating quality in both full- and no-reference scenarios. The proposed method is shown to significantly outperform existing methods, providing enhanced situational awareness in a range of surveillance scenarios.
The immunomodulatory anticancer agent, RRx-001, induces an interferon response through epigenetic induction of viral mimicry (2017)

Transient exposure of HCT 116 cells to low-dose RRx-001 induced transcription of silenced retroviral genes present in the cancer cell DNA with subsequent synthesis of IFN in response to this "pseudo-pathogenic" stimulus, mimicking an antiviral defense. RRx-001-mediated IFN induction may have the potential to improve the efficacy of immunotherapies as well as radiotherapy, standard chemotherapies and molecularly targeted agents when used in combination. The striking safety profile of RRx-001 in comparison to other more toxic epigenetic and immunomodulatory agents such as azacitidine makes it a leading candidate for such clinical applications.
Transcription of Cystic Fibrosis Transmembrane Conductance Regulator Requires a CCAAT-like Element for both Basal and cAMP-mediated Regulation (1995)

The cystic fibrosis transmembrane conductance regulator (CFTR) gene in man is controlled by a tightly regulated and weak promoter. The architecture of the CFTR promoter suggests regulatory characteristics that are consistent with the absence of a TATA-like sequence, including the ability to initiate RNA transcription at numerous positions. Detailed investigation of the most proximal region of the human CFTR gene promoter through deletion and mutational analysis reveals that expression is contingent on the conservation of the inverted CCAAT sequence. Basal expression of CFTR transcription and cAMP-mediated transcriptional regulation require the presence of an imperfect and inverted CCAAT element recognized as 5'-AATTGGAAGCAAAT-3', located between 132 and 119 nucleotides upstream of the translational start site. RNA isolated from a transfected pancreatic cell line carrying integrated wild-type and mutant CFTR-directed transgenes was used to map the 5' termini of the transgenic transcripts. Analysis of the transcript termini by ribonuclease protection analysis reflects the direct association of the conserved inverted CCAAT sequence in promoting transcript initiation. Because of the requirement for the inverted CCAAT sequence for promoting transcription of CFTR, the involvement of CCAAT-binding factors is suspected in the regulation of CFTR gene transcription. To test this, we used electrophoretic mobility shift assays to demonstrate that the majority of the binding to the inverted CCAAT element, between -135 and -116, was easily competed for by binding to cognate nucleotide sequences for CCAAT-enhancer binding protein (C/EBP). An antibody specific for the C/EBP-related protein, C/EBP delta, detected C/EBP delta as part of a nuclear protein complex bound to the inverted CCAAT sequence of the CFTR gene. Also, the detection of specific activating transcription factor/cyclic-AMP response element binding protein antigens by antibody supershift analysis of nuclear complexes suggest that species of this family of transcription factors could be involved in the formation of complexes with C/EBP delta within the CFTR gene inverted CCAAT-like element. These studies raise the possibility of interactions between individual members of the C/EBP and activating transcription factor/cyclic-AMP response element binding protein families potentially contribute to the tight transcriptional control rendered by the CFTR gene promoter.
Preparation of Tamanu Oil Nanoemulsions by Phase Inversion Temperature (2020)

Abstract In this study, the phase inversion temperature (PIT) method was used to prepare a stable tamanu oil nanoemulsion at the lowest surfactant content. The factors affecting the formation of nanoemulsions such as type of surfactant, surfactant to oil ratio (SOR), and water content were investigated. The results showed that Tween 80 is suitable for making a stable nanoemulsion. The SOR is more than or equal to 1.5:1 produced emulsions with particle size less than 100 nm. The particle size decreased as SOR, and water content increased. A higher quantity of surfactant caused higher turbulence and affinity towards the aqueous phase, resulting in smaller droplets. Decreasing droplet size by increasing water content may result from a decreased viscosity of the surfactant at the interface that promotes fluidity and the easy movement of the oil phase towards the aqueous phase. The SOR of 3:1 and water content of 80% were selected due to cost, taste, and toxicity concerns. The impact of storage condition on nanoemulsion stability was also investigated. After one month, samples were stored in the refrigerator had an insignificant increase in absorbance. Particle size analysis also showed a similar result (< 20 nm).
Effect of holding time, temperature and different parenteral solutions on viability and functionality of adult bone marrow-derived mesenchymal stem cells before transplantation (2008)

Mesenchymal stem cells (MSCs) have the ability to proliferate and differentiate into various lineages, given the appropriate microenvironment, thus making MSCs promising candidates for cell transplantation. For clinical applications, MSCs need to be stored in optimal conditions so that they may be transported and made available as an off-the-shelf product for companies to market. Freshly harvested and cultured or frozen-thawed bone marrow-derived MSCs were prepared for cell transplantation. Both freshly cultured or frozen-thawed MSCs were washed and resuspended in parenteral solutions, either 0.9% saline, Dulbecco's phosphate-buffered saline (DPBS), plasmalyte A or 5%dextrose and held for 2, 4, 6 and 8 h at 4 degrees C, 37 degrees C and RT (22 degrees C). The viability of the cells, differentiation capability and expression of cell surface markers were analysed. MSCs harvested from fresh cultures, resuspended in the parenteral solutions and maintained at 4 degrees C for 6 h showed more than 90% viability, and the viability was appreciably better when suspended in 5% dextrose at 4 degrees C for 8 h. In contrast, frozen-thawed cells can be held for a maximum of 2 h after thawing before losing their viability significantly below permissible limits for transplantation. We are reporting for the first time the effect of various parenteral solutions, holding times and temperatures on the viability and functionality of bone marrow-derived freshly cultured or frozen-thawed MSCs for transplantation. Our results suggested that freshly harvested MSCs can be held for 8 h at 4 degrees C in 5% dextrose or for up to 6 h at 4 degrees C in saline, DPBS or plasmalyte A. Freeze-thawed MSCs can be held for a maximum of 2 h in plasmalyte A before transplantation without affecting their viability and ability to differentiate.
Androgen receptor gene expression in human prostate carcinoma cell lines. (1990)

Responses to androgen vary widely among prostate cancers and prostatic carcinoma cell lines. We have explored the basis for this heterogeneity by examining the levels of androgen receptor expression in a prostate carcinoma cell line (LNCaP) that expresses the androgen receptor and two prostate carcinoma cell lines that do not contain detectable androgen receptor. We find that while the LNCaP cell line contains high levels of both the androgen receptor protein and mRNA, the receptor-negative cell lines DU-145 and PC-3 do not express androgen receptor protein as detected by immunoblotting or mRNA as detected by Northern analysis or S1 nuclease protection. These results indicate that the absence of androgen receptor expression in the androgen receptor-negative cell lines is caused by diminished androgen receptor mRNA levels. Genomic Southern analysis indicates that the differences in androgen receptor expression in each of these cell lines is not associated with detectable alterations in the structure of the androgen receptor gene.