gebhart/patrepeval huggingface dataset:
Differential expression in normal-adenoma-carcinoma sequence suggests complex molecular carcinogenesis in colon (2006)

The majority of colon cancers develop from pre-existing adenomas. We analyzed the expression profiles in the sequence of normal colon crypts, adenomas and early-stage carcinomas using microdissected cells from tubular adenomas with foci of malignant transformation. Differentially expressed genes were detected between normal-adenoma and adenoma-carcinoma, and were grouped according to the patterns of expression changes in the sequence. Down-regulated genes in the sequence included PLA2G2A, TSPAN1, PDCD4, FCGBP, AATK, EPLIN, FABP1, AGR2, MTUS1, TSC1, galectin 4 and MT1F. PLA2G2A has been shown to suppress colon tumorigenesis in mice, but the pathobiological role in humans has been controversial. Our data showed continuous down-regulation of PLA2G2A in the sequence supporting an implication in human colon cancer. Tumor suppressor and/ or proapoptotic activities have also been reported in other genes. Up-regulated genes included ribosomal proteins, IER3 and TPR. TGF-beta2 and matrix metalloproteinase 23B were up-regulated in carcinoma but not in adenoma, supporting the pathobiological roles in malignant transformation. Differentially expressed genes partly coincided with those in the adenoma-carcinoma sequence of the stomach, which was published previously, suggesting a partial overlap between the adenoma-carcinoma sequences of the colon and stomach.
Comprehensive analysis of risk factors for seizures after deep brain stimulation surgery (2011)

These results affirm that seizures are an uncommon complication of DBS surgery and generally occur within 48 hours of surgery. The results also indicate that hemorrhage, edema, or ischemia on postoperative images ("abnormal" imaging findings) increases the relative risk of postoperative seizures by 30- to 50-fold, providing statistical credence to the long-held assumption that seizures are associated with intracranial vascular events. Even in the setting of a postimplantation imaging abnormality, long-term anticonvulsant therapy will not likely be required because none of our patients developed chronic epilepsy.
349. Nitrosoacylarylamines. Part V. The nitrosation of 3-acetamido-4-quinolones and -quinaldones (1951)

W. J. Adams and D. H. Hey, J. Chem. Soc., 1951, 1521 DOI: 10.1039/JR9510001521
Monocyte suppressing action of fenofibrate. (2006)

Since atherosclerosis has been proven to be an inflammatory disease, it is obvious that the proper treatment for dyslipidemia should not only correct lipid parameters but also inhibit inflammation. Monocytes and monocyte-derived proinflammatory cytokines are widely known to be involved in the formation and rupture of the atherosclerotic plaque. The aim of our study was to assess the effect of fenofibrate, a commonly used hypolipidemic drug, on the release of interleukin 1beta (IL-1beta), interleukin 6 (IL-6) and monocyte chemoattractant protein 1 (MCP-1) by monocytes from patients with combined hyperlipidemia. Fourteen patients with biochemically confirmed type IIb dyslipidemia who did not respond to a low-fat diet were treated with micronized fenofibrate for 1 month. The control group included 12 healthy, normolipidemic, age-matched subjects. To accurately evaluate the levels of the inflammatory cytokines, we excluded patients with any inflammatory disease. Monocytes were isolated from peripheral blood before and after the treatment. IL-1beta, IL-6 and MCP-1 release was measured by enzyme-linked immunosorbent assay (ELISA) after lipopolysaccharide stimulation. IL-1beta, IL-6 and MCP-1 levels were significantly higher in hyperlipidemic patients compared to the control (143.9 +/- 6.5 vs. 74.4 +/- 4.4 pg/ml; 8212 +/- 285 vs. 6110 +/- 170 pg/ml; 19.6 +/- 0.9 vs. 12.3 +/- 0.6 ng/ml, respectively). Thirty-day fenofibrate treatment decreased the release of IL-1beta by 43% (143.9 +/- 6.5 vs. 86.2 +/- 5.9 pg/ml), of IL-6 by 22% (8212 +/- 285 vs. 6330 +/- 234 pg/ml), and of MCP-1 by 29% (19.6 +/- 0.9 vs. 14.0 +/- 0.8 ng/ml). The evaluated cytokines were markedly elevated in patients with type IIb dyslipidemia. Effective fenofibrate therapy had a significant inhibitory effect on the release of monocyte-derived inflammatory cytokines.
Phase-Transfer Catalyzed Addition of Hydrogen Cyanide to<i>N</i>-Substituted Hydrazones (1990)

In a two-phase system consisting of aqueous sodium cyanide and an inert organic solvent and containing a phase-transfer catalyst, ketone benzoylhydrazones, tosylhydrazones, and methoxycarbonylhydrazones upon addition of acetic acid readily add hydrogen cyanide to give 2-substituted 1-(1-cyanoalkyl)hydrazines.
Targeting neuroinflammation in Alzheimer&rsquo;s disease (2016)

Almost 47 million people suffer from dementia worldwide, with an estimated new case diagnosed every 3.2 seconds. Alzheimer's disease (AD) accounts for approximately 60%-80% of all dementia cases. Given this evidence, it is clear dementia represents one of the greatest global public health challenges. Currently used drugs alleviate the symptoms of AD but do not treat the underlying causes of dementia. Hence, a worldwide quest is under way to find new treatments to stop, slow, or even prevent AD. Besides the classic targets of the oldest therapies, represented by cholinergic and glutamatergic systems, β-amyloid (Aβ) plaques, and tau tangles, new therapeutic approaches have other targets. One of the newest and most promising strategies is the control of reactive gliosis, a multicellular response to brain injury. This phenomenon occurs as a consequence of a persistent glial activation, which leads to cellular dysfunctions and neuroinflammation. Reactive gliosis is now considered a key abnormality in the AD brain. It has been demonstrated that reactive astrocytes surround both Aβ plaques and tau tangles. In this condition, glial cells lose some of their homeostatic functions and acquire a proinflammatory phenotype amplifying neuronal damage. So, molecules that are able to restore their physiological functions and control the neuroinflammatory process offer new therapeutic opportunities for this devastating disease. In this review, we describe the role of neuroinflammation in the AD pathogenesis and progression and then provide an overview of the recent research with the aim of developing new therapies to treat this disorder.
A study on proteins contained in urine of gestosis patients. (1983)

Immunologic analyses of urinary proteins in patients with gestosis and related obstetrical conditions were performed and urinary protein patterns were compared with blood plasma protein patterns. Many kinds of proteins could be detected in urine of patients with gestosis beside albumin. Therefore, "proteinuria" should be chosen to characterise this state instead of the term "albuminuria". Generally speaking, when a total volume of protein contained in urine increases, its types or subfractions also increase in urine. Next to albumin, the most commonly detected proteins in urine of patients with gestosis were transferrin, IgG, inter-alpha-trypsin inhibitor, alpha 1-antitrypsin, IgA, alpha 2-HS-glycoprotein, alpha 1-acid glycoprotein, Gc-globulin, alpha 1-antichymotrypsin, hemopexin, ceruloplasmin, prealbumin, haptoglobin, anti-thrombin III, Cl-inactivator, IgM, and alpha 2-macroglobulin, in the descending order of their occurrence. Proteins that promptly became negative in urine of gestosis patients after delivery were inter-alpha-trypsin inhibitor, IgA, and ceruloplasmin. On the other hand, proteins most apt to persist in urine were albumin, alpha 2-HS-glycoprotein, and IgG. Generally speaking, lower molecular weight proteins were likely to persist in urine after delivery. Simultaneous determination of blood plasma and urinary proteins was performed for 18 kinds or subfractions of protein. A prognostic value of renal protein clearance was discussed.
The growth of reovirus 3 in cultured rat embryos and implications for human reproductive failure. (1983)

Ten-day rat embryos were exposed to different concentrations of reovirus 3, heat-inactivated virus or diluent and then cultured for 48 h. An effect on embryonic growth and development was observed that required live virus. Virus concentrations of 10(6.0) TCID50 were embryolethal while 10(5.0) TCID50 killed about 20% of embryos and caused varying degrees of growth retardation in the remainder. Growth of the agent in the visceral yolk sac and embryonic tissues was confirmed by virus titration and immunofluorescent studies. Infectious virus was detected in the medium after 6-8 h and increased exponentially throughout the 48 h culture period, except for a check around 18 h. The significance of the findings in relation to previous animal studies and the potential importance of reovirus as a cause of human reproductive failure are discussed.
Toxicokinetics of ibogaine and noribogaine in a patient with prolonged multiple cardiac arrhythmias after ingestion of internet purchased ibogaine (2017)

We demonstrated a linear relationship between the concentration of the metabolite and long duration of action, rather than with parent ibogaine. Therefore, after (prolonged) ibogaine ingestion, clinicians should beware of long-term effects due to its metabolite.
Comment on ‘‘Theory of photon bands in three-dimensional periodic dielectric structures’’ (1991)

A Comment on the Letter by Satpathy, Zhang, and Salehpour, Phys. Rev. Lett. 64, 1239 (1990).
Outcomes of initiation of therapy with once‐daily combination of a thiazolidinedione and a biguanide at an early stage of type 2 diabetes (2004)

Early initiation of therapy for type 2 diabetes with a once-daily combination of metformin and rosiglitazone provides the greatest opportunity to achieve A1cs within the normal range. The level of achieved glycaemic control is not dependent on the number or potency of the therapies utilized but is dependent on the level of endogenous insulin production. The use of a TZD as part of initial therapy of type 2 diabetes with its documented ability to preserve or improve beta-cell function has the potential to achieve prolonged normoglycaemia in the type 2 diabetic patient.
Dopamine in Drug Abuse and Addiction (2007)

Imaging studies have provided new insights on the role of dopamine (DA) in drug abuse and addiction in the human brain. These studies have shown that the reinforcing effects of drugs of abuse in human beings are contingent not just on DA increases per se in the striatum (including the nucleus accumbens) but on the rate of DA increases. The faster the increases, the more intense the reinforcing effects. They have also shown that elevated levels of DA in the dorsal striatum are involved in the motivation to procure the drug when the addicted subject is exposed to stimuli associated with the drug (conditioned stimuli). In contrast, long-term drug use seems to be associated with decreased DA function, as evidenced by reductions in D2 DA receptors and DA release in the striatum in addicted subjects. Moreover, the reductions in D2 DA receptors in the striatum are associated with reduced activity of the orbitofrontal cortex (region involved with salience attribution and motivation and with compulsive behaviors) and of the cingulate gyrus (region involved with inhibitory control and impulsivity), which implicates deregulation of frontal regions by DA in the loss of control and compulsive drug intake that characterizes addiction. Because DA cells fire in response to salient stimuli and facilitate conditioned learning, their activation by drugs will be experienced as highly salient, driving the motivation to take the drug and further strengthening conditioned learning and producing automatic behaviors (compulsions and habits).
CD44H expression by human neuroblastoma cells: relation to MYCN amplification and lineage differentiation. (1994)

The human CD44 cell surface glycoprotein has been involved in a variety of functions including lymphocyte homing, extracellular cell matrix attachment, and tumor metastasis. Due to the alternative splicing of the single gene, a large family of different variants or isoforms is generated. Several reports have indicated an up-regulation of CD44 variant (v) isoforms in malignant process, conferring metastatic potential to non-metastatic cells. Neuroblastoma is a tumor characterized by an aggressive and metastatic behavior in advanced stages with amplification of the MYCN protooncogene. In this report we show that the CD44 standard molecule is highly expressed in 100% of stage I-III, IVs neuroblastomas and ganglioneuromas but only in a subset of stage IV tumors. In contrast, no expression of CD44 was detected on MYCN amplified stage IV tumors, thus demonstrating a highly significant negative relationship between MYCN amplification and CD44 expression in neuroblastoma. The expression of CD44 on neuroblastoma cultured cell lines was not shown to be related to MYCN amplification but rather linked to the S-type, schwann/glial differentiation lineage. Immunochemical analysis of tumor samples with anti-CD44v3 and -v6 antibodies and Northern blot analysis of mRNA from cell lines with probes spanning exons 4-10 did not reveal any expression of splice variants on neuroblastomas of all stages and cell lines, thus ruling out a major role of these isoforms in neuroblastoma progression and metastasis.
Panel I: Current U.S. Drug Policy and Alternative Paradigms (2010)

Moderator: Hon. James Rogan, Orange County Superior Court Judge Hector Berrellez, former DEA Agent and Terrorism Expert Hon. Jim Gray, former Orange County Superior Court Judge Asa Hutchinson, former Director of DEA and Under Secretary for Homeland Security Alex Kreit, Thomas Jefferson School of Law
Integrated network model provides new insights into castration-resistant prostate cancer (2015)

Castration-resistant prostate cancer (CRPC) is the main challenge for prostate cancer treatment. Recent studies have indicated that extending the treatments to simultaneously targeting different pathways could provide better approaches. To better understand the regulatory functions of different pathways, a system-wide study of CRPC regulation is necessary. For this purpose, we constructed a comprehensive CRPC regulatory network by integrating multiple pathways such as the MEK/ERK and the PI3K/AKT pathways. We studied the feedback loops of this network and found that AKT was involved in all detected negative feedback loops. We translated the network into a predictive Boolean model and analyzed the stable states and the control effects of genes using novel methods. We found that the stable states naturally divide into two obvious groups characterizing PC3 and DU145 cells respectively. Stable state analysis further revealed that several critical genes, such as PTEN, AKT, RAF, and CDKN2A, had distinct expression behaviors in different clusters. Our model predicted the control effects of many genes. We used several public datasets as well as FHL2 overexpression to verify our finding. The results of this study can help in identifying potential therapeutic targets, especially simultaneous targets of multiple pathways, for CRPC.
Fracture prevention by femoroplasty—cement augmentation of the proximal femur (2011)

The prevention of hip fractures is a desirable goal to reduce morbidity, mortality, and socio-economic burden. We evaluated the influence on femoral strength of different clinically applicable cementing techniques as "femoroplasty." Twenty-eight human cadaveric femora were augmented by means of four clinically applicable percutaneous cementing techniques and then tested biomechanically against their native contralateral control to determine fracture strength in an established biomechanical model mimicking a fall on the greater trochanter. The energy applied until fracture could be significantly increased by two of the methods by 160% (53.1 Nm vs. 20.4 Nm, p < 0.001) and 164% (47.1 Nm vs. 17.8 Nm, p = 0.008), respectively. The peak load to failure was significantly increased by three of the methods by 23% (3818.3 N vs. 3095.7 N, p = 0.003), 35% (3698.4 N vs. 2737.5 N, p = 0.007), and 12% (3056.8 N vs. 2742.8 N, p = 0.005), respectively. The femora augmented with cemented double drill holes had a lower fracture strength than the single drilled ones. Experimental femoroplasty is a technically feasible procedure for the prophylactic reinforcement of the osteoporotic proximal femur and, hence, could be an auxiliary treatment option to protect the proximal femur against osteoporotic fractures.
Special size effects in advanced single-gate and multiple-gate SOI transistors (2007)

State-of-the-art SOI transistors require a very small body. This paper examines the effects of body thinning and thin-gate oxide in SOI MOSFETs on their electrical characteristics. In particular, the influence of film thickness on the interface coupling and carrier mobility is discussed. Due to coupling, the separation between the front and back channels is difficult in ultra-thin SOI MOSFETs. The implementation of the front-gate split C-V method and its limitations for determining the front- and back-channel mobility are described. The mobility in the front channel is smaller than that in the back channel due to additional Coulomb scattering. We also discuss the 3D coupling effects that occur in FinFETs with triple-gate and omega-gate configurations. In low-doped or tall fins the corner effect is suppressed. Narrow devices are virtually immune to substrate effects due to a strong lateral coupling between the two lateral sides of the gate. Short-channel effects are drastically reduced when the lateral coupling screens the drain influence.
Reaction of β-propiolactone with amino acids and its specificity for methionine (1968)

1. The reactions of beta-propiolactone with amino acids were investigated under various conditions of pH and temperature to find those under which the reagent acted with specificity. 2. At pH9.0 and 22 degrees , after 15min. of reaction, at least 85% of each amino acid had reacted, methionine and cystine being the most reactive. 3. At pH7.0 and 22 degrees most amino acids reacted; methionine, cystine and histidine reacted almost entirely, and proline and lysine to a significantly smaller extent. 4. At pH3.0 and 22 degrees further specificity was obtained; methionine and cystine were the only reactive amino acids. 5. Reaction at pH3.0 and 0 degrees was specific for methionine; it was the only amino acid modified even after 145hr. of reaction.
A Model of Allergic Nasal Congestion in Dogs Sensitized to Ragweed (2003)

These results suggest that the canine model may be used to study upper-airway diseases such as allergic rhinitis and to evaluate the pharmacologic activity of nasal decongestants.
The protein scaffold of the lipocalin odorant-binding protein is suitable for the design of new biosensors for the detection of explosive components (2007)

The detection of hazard exposure is a current priority, including the detection of traces of explosive molecules in different environments like luggage storage rooms and public places, and is becoming a major requirement for homeland security. In the present study we carried out a preliminary investigation on the binding capacities of four forms of the lipocalin odorant- binding protein ( OBP) for the detection of explosive components such as diphenylamine, dimethylphthalate, resorcinol and dinitrotoluene. The experimental results, showing that OBP binds these compounds with affinity constants ranging between 80 nM and 10.6 mM, indicate that this protein can be used as a probe for the realization of a biosensor to sense explosive compounds.
The Finite Screw System Associated With the Displacement of a Line (2003)

In determining the screw systems associated with incompletely specified displacements, the displacement of a line was known to be an exceptional case. Recent research has concluded that all possible screws for the finite displacement of a line do not form a screw system. This paper utilizes Dimentberg’s definition of pitch to demonstrate that all possible screws for displacing a line from one position to another can indeed form a screw system of the third order. Two different approaches are taken: one uses the concept of a screw triangle, and the other is based on analytical geometry. A set of three linearly independent screws of the screw system is shown to be perpendicularly intersecting the external bisector of the initial and final positions of the line.
Thermally robust cu interconnects with Cu-Ag alloy for sub 45nm node (2005)

Cu interconnects reliability has been drastically improved by the introduction of Ag doped Cu (Cu-Ag) alloy seed. The usage of Cu-Ag remarkably suppressed stress induced voiding (SiV) in the lower wide metal which appeared by the additional anneal to prevent the degradation of the barrier metal. It has been explained by the Cu extrusion model where the void formation was caused by the poor adhesion between the upper barrier metal and the extruded lower metal under the via. The thermal stress hysteresis curve of Cu-Ag which shows the shift of the softening temperature to higher suggests more thermal resistance to Cu extrusion than pure Cu. Also no degradation of interconnects performance and the minimum increase of the resistance were verified. These indicate that Cu-Ag alloy is the most feasible candidate for the improvement of the reliability issues of Cu interconnects with porous low-k film for 45nm node and beyond.
In Our Own Image: Personal Symmetry in Discovery (2001)

I gave lectures entitled "Ugly Symmetry" at several conferences and many institutes during past six years.[...]
Supported palladium membrane reactor architecture for electrocatalytic hydrogenation (2019)

Sputtering palladium onto a porous PTFE support enables a 96% reduction in metal content in an electrolytic palladium membrane reactor.
Photoresist cross-sectional shape change caused by scanning electron microscope-induced shrinkage (2015)

Change in the cross-sectional profile of a photoresist (PR) pattern due to shrinkage was evaluated to investigate the mechanism of electron beam-induced shrinkage. A scanning transmission electron microscope (STEM) was used to observe the cross-sectional profiles of PR lines after atomic-layer deposition of metal oxide and carbon deposition on the sample surface. A HfO2 thin layer enhanced the profile contrast in the STEM measurements without blurring the edge, which enabled the precise cross-sectional measurement of the PR patterns. We found interesting features associated with shrinkage from the detailed profile change obtained using this method, such as a rounding of the pattern top, a necking of the sidewall profile, a rounding of the foot in the pattern on the organic underlying layer, and voltage-independent sidewall shrinkage under a large electron beam dose. These behaviors along with the results from a Monte Carlo simulation are discussed. Consequently, these observations experimentally clarified that the elastic deformation effect and the impact of the secondary electrons emitted from the spaces around the pattern into the sidewall are important to interpret the change in the shape of the pattern induced by shrinkage.
Single-Strand-Specific Nucleases (1995)

Single-strand-specific nucleases, which act on single-stranded nucleic acids and single-stranded regions in double-stranded nucleic acids, are multifunctional enzymes and are ubiquitous in distribution. They find wide application as analytical tools in molecular biology research, although enzymes such as P1 nuclease are also used for production of flavor enhancers such as 5′ IMP and 5′ GMP. Because these enzymes are mainly used as analytical tools, very little attention was paid to aspects relating to their structure-function relationships. However, during the last few years considerable developments have taken place in this area. Single-strand-specific nucleases, their purification, characteristics, biological role, and applications have been reviewed.