gebhart/patrepeval huggingface dataset:
A Bacillus thuringiensis subsp. israelensis gene encoding a 125-kilodalton larvicidal polypeptide is associated with inverted repeat sequences (1988)

A gene encoding a 125-kilodalton (kDa) mosquitocidal delta-endotoxin was cloned from the 72-MDa resident plasmid of Bacillus thuringiensis subsp. israelensis. This gene is similar in its 3' region to the gene encoding the 135-kDa protein previously cloned (C. Bourgouin, A. Klier, and G. Rapoport, Mol. Gen. Genet. 205:390-397, 1986). Escherichia coli recombinant clones harboring the 125-kDa gene were toxic to larvae of the three mosquito species Aedes aegypti, Anopheles stephensi, and Culex pipiens. In addition, the B. thuringiensis subsp. israelensis DNA fragment carrying the 125-kDa protein gene contains two sets of inverted repeat sequences, identified either by the S1 nuclease method or by electron microscopic observation. The structural organization of inverted repeat sequences and of the 125-kDa gene was analyzed and suggests that this B. thuringiensis subsp. israelensis delta-endotoxin gene is located within a transposable element.
The Marmousi experience: Velocity model determination on a synthetic complex data set (1994)

The motivation behind seismic data acquisition and processing is simple—to obtain a depth image of the earth—but performing this process correctly is extremely difficult. A number of well known processing tasks (such as static corrections, deconvolution, multiple elimination, velocity estimation, and migration) have to be executed, and each directly influences the final result. However, the success of the velocity estimation is paramount and critical, and large amounts of man/CPU hours are devoted to it.
Computer Generation of Structural Models of Amorphous Si and Ge (1985)

We have developed and applied a computer algorithm that generates realistic random-network models of $a$-Si with periodic boundary conditions. These are the first models to have correlation functions that show no serious discrepancy with experiment. The algorithm provides a much-needed systematic approach to model construction that can be used to generate models of a large class of amorphous materials.
Antiretroviral drug treatment for HIV/AIDS. (1996)

As new antiretroviral drugs for the treatment of human immunodeficiency virus (HIV) infection and new tests to measure HIV infection have become available, primary care clinicians now have more management options than ever before. Viral load measurements are becoming more accepted as a means of assessing HIV disease and estimating the efficacy of specific drug regimens. Clinical status changes also mark times to review antiretroviral regimens. Potential benefits of combination drug therapy, including the new protease inhibitor class of drugs, have added a new sense of optimism to the care of patients with HIV. Whether combination therapy and protease inhibitor treatment will live up to their promise by inducing better long-term clinical results remains to be seen.
Neurobiological and psychiatric consequences of child abuse and neglect (2010)

The effects of early-life trauma and its consequences for the treatment of depression are reviewed. The prevalence and clinical sequelae of early sexual and physical abuse, neglect and parental loss are described. An overview of preclinical studies that help guide clinical research and practice is presented. Human clinical studies on the neurobiological consequences of early trauma are summarized. Moderating factors, such as genetic variation and sex differences, are discussed. The few current treatment outcome studies relevant to this research area are described. Guidance for the management of patients with depression and a history of child abuse and neglect are provided. Most patients who have experienced early traumatic experiences are likely best treated with a combination of psychotherapy and pharmacotherapy. This review is dedicated to the memory of Seymour Levine who pioneered the field of early experience research and to a considerable extent inspired the clinical studies described in this review.
Discovery of the gene signature for acute lung injury in patients with sepsis (2009)

The acute respiratory distress syndrome (ARDS)/acute lung injury (ALI) was described 30 yr ago, yet making a definitive diagnosis remains difficult. The identification of biomarkers obtained from peripheral blood could provide additional noninvasive means for diagnosis. To identify gene expression profiles that may be used to classify patients with ALI, 13 patients with ALI + sepsis and 20 patients with sepsis alone were recruited from the Medical Intensive Care Unit of the University of Pittsburgh Medical Center, and microarrays were performed on peripheral blood samples. Several classification algorithms were used to develop a gene signature for ALI from gene expression profiles. This signature was validated in an independently obtained set of patients with ALI + sepsis (n = 8) and sepsis alone (n = 1). An eight-gene expression profile was found to be associated with ALI. Internal validation found that the gene signature was able to distinguish patients with ALI + sepsis from patients with sepsis alone with 100% accuracy, corresponding to a sensitivity of 100%, a specificity of 100%, a positive predictive value of 100%, and a negative predictive value of 100%. In the independently obtained external validation set, the gene signature was able to distinguish patients with ALI + sepsis from patients with sepsis alone with 88.9% accuracy. The use of classification models to develop a gene signature from gene expression profiles provides a novel and accurate approach for classifying patients with ALI.
Knowledge acquisition tools based on personal construct psychology (1993)

Abstract Knowledge acquisition research supports the generation of knowledge-based systems through the development of principles, techniques, methodologies and tools. What differentiates knowledge-based system development from conventional system development is the emphasis on in-depth understanding and formalization of the relations between the conceptual structures underlying expert performance and the computational structures capable of emulating that performance. Personal construct psychology is a theory of individual and group psychological and social processes that has been used extensively in knowledge acquisition research to model the cognitive processes of human experts. The psychology takes a constructivist position appropriate to the modelling of human knowledge processes, but develops this through the characterization of human conceptual structures in axiomatic terms that translate directly to computational form. In particular, there is a close correspondence between the intensional logics of knowledge, belief and action developed in personal construct psychology, and the intensional logics for formal knowledge representation developed in artificial intelligence research as term subsumption, or KL-ONE-like, systems. This paper gives an overview of personal construct psychology and its expression as an intensional logic describing the cognitive processes of anticipatory agents, and uses this to survey knowledge acquisition tools deriving from personal construct psychology.
The effect of smoking on MAOA promoter methylation in DNA prepared from lymphoblasts and whole blood (2009)

Prior work using lymphoblast DNA prepared from 192 subjects from the Iowa Adoption Studies (IAS) demonstrated that decreased MAOA promoter methylation was associated with lifetime symptom count for nicotine dependence (ND) and provided suggestive evidence that the amount of methylation is genotype dependent. In the current investigation, we replicate and extend these prior findings in three ways using another 289 IAS subjects and the same methodologies. First, we show that methylation is dependent on current smoking status. Second, we introduce a factor analytic approach to DNA methylation, highlighting three distinct regions of the promoter that may function in somewhat different ways for males and females. Third, we directly compare the methylation signatures in DNA prepared from whole blood and lymphoblasts from a subset of these subjects and provide suggestive evidence favoring the use of lymphoblast DNA. We conclude that smoking reliably decreases MAOA methylation, but exact characterization of effects on level of methylation depend on genotype, smoking history, current smoking status, gender, and region of the promoter-associated CpG Island examined.
Long-term survival of dogs with advanced malignant melanoma after DNA vaccination with xenogeneic human tyrosinase: a phase I trial. (2003)

The results of this trial demonstrate that xenogeneic DNA vaccination of dogs with advanced malignant melanoma is a safe and potentially therapeutic modality. On the basis of these results, additional evaluation of this novel therapeutic is warranted in locally controlled CMM and advanced human melanoma.
Killing from within (2012)

Interleukin-10 (IL-10) is considered to be an immunosuppressive cytokine. However, the continuous administration of pegylated IL-10 (PEG-IL10) leads to the rejection of large, firmly established and metastatic syngeneic tumors. PEG-IL10 therapy induces the expansion and activation of intratumoral, tumor antigen-specific CD8(+) T cells, leading to interferon γ (IFNγ)-mediated Th1 like immunity and tumor rejection.
Increase in percutaneous muscle biopsy yield with a suction-enhancement technique (1997)

The percutaneous muscle biopsy technique is used in clinical practice and biomedical research. We developed a new enhanced-suction technique [suction-enhancing nipples (SEN)] and compared it with techniques currently in practice by assessing biopsy yields on anesthetized pigs. We applied the enhanced-suction technique to human subjects participating in a clinical trial. In the pig, there was a mean 91% (1.9-fold) increase in the size of the samples obtained with the 4-mm needle when SEN was used and a mean 507% (fivefold) increase in sample size when the SEN was applied to the 6-mm needles. Nine passes of the 6-mm needle with SEN obtained from five consecutive human subjects yielded a mean individual sample size of 109.4 mg or 219.4 mg per needle pass when using the double-sample technique. Adequate tissue samples for histomorphometric and other analyses were obtained in all samples obtained. The percutaneous muscle biopsy performed with enhanced suction using inexpensive, readily available nipples enhances tissue yield two- to fivefold.
Selective HDAC Inhibition for the Disruption of Latent HIV-1 Infection (2020)

Selective histone deacetylase (HDAC) inhibitors have emerged as a potential anti-latency therapy for persistent human immunodeficiency virus type 1 (HIV-1) infection. We utilized a combination of small molecule inhibitors and short hairpin (sh)RNA-mediated gene knockdown strategies to delineate the key HDAC(s) to be targeted for selective induction of latent HIV-1 expression. Individual depletion of HDAC3 significantly induced expression from the HIV-1 promoter in the 2D10 latency cell line model. However, depletion of HDAC1 or −2 alone or in combination did not significantly induce HIV-1 expression. Co-depletion of HDAC2 and −3 resulted in a significant increase in expression from the HIV-1 promoter. Furthermore, concurrent knockdown of HDAC1, −2, and −3 resulted in a significant increase in expression from the HIV-1 promoter. Using small molecule HDAC inhibitors of differing selectivity to ablate the residual HDAC activity that remained after (sh)RNA depletion, the effect of depletion of HDAC3 was further enhanced. Enzymatic inhibition of HDAC3 with the selective small-molecule inhibitor BRD3308 activated HIV-1 transcription in the 2D10 cell line. Furthermore, ex vivo exposure to BRD3308 induced outgrowth of HIV-1 from resting CD4+ T cells isolated from antiretroviral-treated, aviremic HIV+ patients. Taken together these findings suggest that HDAC3 is an essential target to disrupt HIV-1 latency, and inhibition of HDAC2 may also contribute to the effort to purge and eradicate latent HIV-1 infection.
Targeting of a hydrophilic photosensitizer by use of internalizing monoclonal antibodies: A new possibility for use in photodynamic therapy (2000)

Coupling of photosensitizers to tumor-selective monoclonal antibodies (MAbs) is an attractive option for improving the selectivity of photodynamic therapy (PDT). For this purpose, hydrophilic sensitizers would be most suitable because of their solubility in water. However, such sensitizers are known to be ineffective in PDT, probably because they cannot readily pass the cell membrane and reach the critical intracellular target. We used the model compound TrisMPyP-PhiCO(2)H, a hydrophilic porphyrin derivative, to test the hypothesis that hydrophilic photosensitizers might become of therapeutic value when directed into the tumor cell by use of internalizing MAbs. TrisMPyP-PhiCO(2)H was conjugated using a labile ester. Conjugates showed no impairment of integrity on SDS-PAGE, full stability in serum in vitro, and optimal immunoreactivity when the sensitizer:MAb ratio was </=3. At higher molar ratios, the solubility of the conjugates decreased. In vitro internalization experiments showed that TrisMPyP-PhiCONH-(125)I-cMAb U36 and TrisMPyPPhiCONH-(125)I-mMAb 425 conjugates were internalized by A431 cells, in contrast to TrisMPyP-PhiCONH-(125)I-mMAb E48 conjugates. Data on the in vitro efficacy of PDT with MAb-conjugated TrisMPyP-PhiCO(2)H showed that the internalizing cMAb U36 and mMAb 425 conjugates were phototoxic to A431 cells, while the non-internalizing E48 conjugate and the unconjugated sensitizer were not. Biodistribution data of conjugates with sensitizer:(125)I-cMAb U36 ratios varying from 1:1 to 3:1 in tumor-bearing nude mice revealed selective accumulation in the tumor. Conjugates with higher molar ratios were cleared more rapidly from the blood than the unconjugated (125)I-cMAb U36, resulting in lower tumor uptake but similar tumor-to-blood ratios. Our data suggest that hydrophilic photosensitizers might have therapeutic value when targeted to tumors by internalizing MAbs.
Proliferation, Apoptosis, and Survivin Expression in Keratinocytic Neoplasms and Hyperplasias (2004)

The dysregulation of apoptosis occurs in many cutaneous disease states. Several apoptosis inhibitors have been shown elevated in neoplasms and in some inflammatory conditions, but their relation to proliferative and apoptotic states has not been defined. We examined the expression of the apoptosis inhibitor survivin in a panel of keratinocytic neoplasms and hyperproliferative skin lesions using both immunohistochemistry and a newly developed in situ hybridization technique. Proliferation and apoptotic indices were also assessed by immunohistochemical staining for proliferating cell nuclear antigen and TUNEL, respectively. We found the highest rate of proliferation in verrucae and psoriasis followed by actinic keratosis, squamous and basal cell carcinoma, lichen simplex chronicus, and seborrheic keratosis; all were significantly (P < 0.05) higher than normal skin. Apoptotic rate was increased in squamous (P = 0.05) and basal cell carcinoma (P = 0.03), but not significantly different from normal skin in the other lesions tested. Survivin expression was seen in most neoplasms and hyperproliferative lesions, but not normal skin. Survivin expression was often restricted to the upper third of the epidermis in psoriasis and lichen simplex chronicus, whereas all the other lesions stained diffusely. Survivin expression appears to be a consistent feature of keratinocytic neoplasms and hyperproliferative lesions and may contribute to the formation of epidermal hyperplasia seen in all of these disease states.
Decreased RIZ1 expression but not RIZ2 in hepatoma and suppression of hepatoma tumorigenicity by RIZ1 (1999)

The distal short arm of human chromosome 1 (1p36) is commonly altered in primary hepatoma tumors and cell lines. This region includes the RIZ gene, a member of the PR (PRDI-BF1/BLIMP1 and RIZ homology) domain family of transcription factors. An unusual feature of this family is the yin-yang involvement in human cancers. Two products are normally produced from a PR family member which differ by the presence or absence of the PR domain; the PR-plus product is disrupted or underexpressed whereas the PR-minus product is present or overexpressed in cancer cells. The PR-plus product RIZ1 is a candidate tumor suppressor because it can induce G(2)/M arrest and/or apoptosis and is commonly underexpressed in breast cancer. Here, we have investigated the role of RIZ in hepatoma. RIZ1 transcript was undetectable in 80% of hepatoma cell lines (8 of 10 lines examined). RIZ1 expression was also decreased in hepatoma tumor specimens. In contrast, RIZ2 transcript was uniformly present in all samples examined. Adenovirus-mediated RIZ1 expression in hepatoma cell lines caused cell cycle arrest in G(2)/M and/or programmed cell death. RIZ1 expression also suppressed tumorigenicity of hepatoma cells in nude mice. Our observations reinforce the yin-yang notion of RIZ gene products in human cancer and suggest a RIZ1 tumor suppressor role in hepatoma.
Retinoic Acid Signaling in the Nervous System of Adult Vertebrates (2004)

The majority of the functions of vitamin A are carried out by its metabolite, retinoic acid (RA), a potent transcriptional activator acting through members of the nuclear receptor family of transcription factors. In the CNS, RA was first recognized to be essential for the control of patterning and differentiation in the developing embryo. It has recently come to light, however, that many of the same functions that RA directs in the embryo are involved in the regulation of plasticity and regeneration in the adult brain. The same intricate metabolic control system of synthetic and catabolic enzymes, combined with cytoplasmic binding proteins, is used in both embryo and adult to create regions of high and low RA to modulate gene transcription. This review summarizes some of the discoveries in the new field of retinoid neurobiology including its functions in neural plasticity and LTP in the hippocampus; its possible role in motor disorders such as Parkinson's disease, motoneuron disease, and Huntington's disease; its role in regeneration after sciatic nerve and spinal cord injury; and its possible involvement in psychiatric diseases such as depression.
Laparoscopic Sentinel Lymph Node Biopsy for Prostate Cancer: The Relevance of Locations Outside the Extended Dissection Area (2011)

Objective. To assess the relevance of sentinel lymph nodes (SNs) outside the extended pelvic lymph node dissection area (e-PLND). Patients and Methods. Evaluation of our laparoscopic SN procedures for prostate cancer patients of intermediate prognosis. Retrospective data collection on the exact location of the excised SNs and the pathology results were analyzed. Results and Limitations. Of the 121 patients, 49 had positive lymph nodes. 37 patients (31%) had SNs outside the e-PLND template. Five of these nodes were tumor bearing but only twice exclusively so. Of the 14 patients considered for salvage treatment, 6 were node positive. 7 of these 14 patients (50%) had SNs outside the extended dissection area, yet none of these nodes were tumor positive. Limitations are those of a retrospective study. Conclusions. Laparoscopic SN biopsy may show SNs outside the e-PLND template in 31% of the patients. However, nodes that are exclusively positive in one of these areas are rare. For the dichotomy positive or negative nodes, the locations outside the e-PLND area are not often relevant. Nevertheless, when all positive nodes are to be treated by resection or radiotherapy, these locations are relevant. When considering salvage treatment for prostate cancer, the method is feasible.
Use of a haptic device by blind and sighted people : perception of virtual textures and objects (1998)

This paper describes a series of studies involving a haptic device which can display virtual textures and 3D objects. The device has potential for simulating real world objects and assisting in the navigation of virtual environments (VEs). Three experiments investigated: (a) whether previous results from experiments using real textures could be replicated using virtual textures
Remotely Triggered Release from Magnetic Nanoparticles (2007)

Multifunctional nanoparticles are multivalent, remotely-actuated, and imaged non-invasively. Superparamagnetic nanoparticles transduce external electromagnetic energy to heat, thereby melting oligonucleotide duplexes that act as tunable, heat-labile tethers to release model drugs in vivo (see figure).
Hemp Extract with Specific Anti‐Cancer Properties against Ovarian Cancer (2021)

Ovarian cancer is one of the most aggressive gynecological cancers (Matz et al., 2017) and the fifth leading cause of cancer‐related deaths among women (Siegel et al., 2015; American Cancer Society, 2019). The current treatment options include Cisplatin and Liposomal Doxorubicin. However, due to limited efficacy and unwanted side effects of the existing therapeutics, it is important to look for alternative therapies. Due to growing interest in medicinal treatments with natural substances, we began a search for natural products with anti‐cancer activity. Most of the existing literature is about the use of medical cannabis or Dronabinol for cancer‐related side effects management. Some other studies are beginning to emerge on the anti‐cancer effects of certain cannabinoids or mixtures of cannabinoids on few cancers. However, no one has reported the anti‐cancer properties on Hemp Extract (HE) that we utilized. The objective of this study is to investigate whether HE has anti‐cancer properties against ovarian cancer cells (OCCs) while being safe to normal ovary epithelial cells (NHOECs). Our specific aims were to investigate 1) Dose response relationship and half maximal effective concentration (EC 50) for HE; 2) HE's ability to specifically decrease ovarian cancer cell (OCC) viability; 3) Specifically cause cytotoxicity to OCCs; 4) Specifically decrease OCC death; and 5) Decrease metastasis of OCCs. Our methods include preparation and purification of HE, cannabinoid amount and molarity calculations, cell culture, HE Treatments, EC 50 calculations, and multiple cell‐based assays / detection methods including cell viability assays (MTT, CALCEIN), cell death detection (ETHD‐1), apoptosis assays (CASPASE), phase contrast microscopy, cytotoxicity assays (LDH), and the cell migration assay. The HE was produced using supercritical carbon dioxide extraction method and given to the laboratory. This extract was made from the flowers, stalks, and leaves of the seedless hemp plants. HE stocks and different working concentrations were made and purified in the laboratory. We have treated cultured OCCs (A2780 and MES‐OV) and NHOECs with different concentrations of HE for 24 hours. Cannabinoid amounts and molarity present in each hemp treatment concentration were calculated. Dose repose relationships were established, and EC 50 was calculated for A2780 OCCs treated with HE. Several cell‐based assays were conducted to fulfill each of the specific aims. We found that the EC 50 value of the HE equals to 13.59 µg/ml HE (containing 12.5 µM total CBD), HE caused OCC specific death, caused OCC specific cytotoxicity, and attenuated OCC proliferation while being safe to NHOECs. HE also decreased OCC migration. Here we concluded that HE has specific anti‐cancer activity against ovarian cancer while being safe to NHOECs. To the best of our knowledge, the ovarian cancer‐cell specific anti‐cancer properties of HE has not been reported to date. The mechanisms behind this specific anti‐cancer properties are currently under investigation.