gebhart/patrepeval huggingface dataset:
5′ Phospholipid Phosphatase SHIP-2 Causes Protein Kinase B Inactivation and Cell Cycle Arrest in Glioblastoma Cells (2000)

The tumor suppressor protein PTEN is mutated in glioblastoma multiform brain tumors, resulting in deregulated signaling through the phosphoinositide 3-kinase (PI3K)-protein kinase B (PKB) pathway, which is critical for maintaining proliferation and survival. We have examined the relative roles of the two major phospholipid products of PI3K activity, phosphatidylinositol 3,4-biphosphate [PtdIns(3,4)P2] and phosphatidylinositol 3,4,5-triphosphate [PtdIns(3,4,5)P3], in the regulation of PKB activity in glioblastoma cells containing high levels of both of these lipids due to defective PTEN expression. Reexpression of PTEN or treatment with the PI3K inhibitor LY294002 abolished the levels of both PtdIns(3, 4)P2 and PtdIns(3,4,5)P3, reduced phosphorylation of PKB on Thr308 and Ser473, and inhibited PKB activity. Overexpression of SHIP-2 abolished the levels of PtdIns(3,4,5)P3, whereas PtdIns(3,4)P2 levels remained high. However, PKB phosphorylation and activity were reduced to the same extent as they were with PTEN expression. PTEN and SHIP-2 also significantly decreased the amount of PKB associated with cell membranes. Reduction of SHIP-2 levels using antisense oligonucleotides increased PKB activity. SHIP-2 became tyrosine phosphorylated following stimulation by growth factors, but this did not significantly alter its phosphatase activity or ability to antagonize PKB activation. Finally we found that SHIP-2, like PTEN, caused a potent cell cycle arrest in G(1) in glioblastoma cells, which is associated with an increase in the stability of expression of the cell cycle inhibitor p27(KIP1). Our results suggest that SHIP-2 plays a negative role in regulating the PI3K-PKB pathway.
A comparative study of the N-linked oligosaccharide structures of human IgG subclass proteins (1990)

Quantitative oligosaccharide profiles were determined for each of 18 human IgG paraproteins representing the four subclasses. Each paraprotein exhibits a unique profile that may be substantially different from that observed for polyclonal IgG. The IgG2 and some IgG3 proteins analysed exhibit a predominance of oligosaccharide moieties having galactose on the Man(alpha 1----3) arm rather than the Man(alpha 1----6) arm; it was previously held that galactosylation of the Man(alpha 1----6) arm is preferred, as observed for IgG1, IgG4 and polyclonal IgG. An IgG4 protein is reported that has galactosylated Man(alpha 1----3) and Man(alpha 1----6) arms on both Fc-localized carbohydrate moieties; previous findings suggested that such fully glycosylated structures could not be accommodated within the internal space of the C gamma 2 domains. Unusual monoantennary oligosaccharides present in IgG2 and IgG3 proteins were isolated and their structures determined.
Fluorescence Intermittency in Single InP Quantum Dots (2001)

Fluorescence “blinking” kinetics of isolated colloidal InP quantum dots (QDs) are investigated via confocal single molecule microscopy. Analysis of fluorescence trajectories reveals inverse power law behavior (∝ 1/τm) in on/off time probability densities with mon ≈ 2.0(2) and moff ≈ 1.5(1). Such an inverse power law in both on/off times is inconsistent with a static distribution of electron/hole trapping sites and highlights the role of fluctuations in the QD nanoenvironment.
Molecular genetics of bipolar disorder and depression (2007)

In this review, all papers relevant to the molecular genetics of bipolar disorder published from 2004 to the present (mid 2006) are reviewed, and major results on depression are summarized. Several candidate genes for schizophrenia may also be associated with bipolar disorder: G72, DISC1, NRG1, RGS4, NCAM1, DAO, GRM3, GRM4, GRIN2B, MLC1, SYNGR1, and SLC12A6. Of these, association with G72 may be most robust. However, G72 haplotypes and polymorphisms associated with bipolar disorder are not consistent with each other. The positional candidate approach showed an association between bipolar disorder and TRPM2 (21q22.3), GPR50 (Xq28), Citron (12q24), CHMP1.5 (18p11.2), GCHI (14q22-24), MLC1 (22q13), GABRA5 (15q11-q13), BCR (22q11), CUX2, FLJ32356 (12q23-q24), and NAPG (18p11). Studies that focused on mood disorder comorbid with somatic symptoms, suggested roles for the mitochondrial DNA (mtDNA) 3644 mutation and the POLG mutation. From gene expression analysis, PDLIM5, somatostatin, and the mtDNA 3243 mutation were found to be related to bipolar disorder. Whereas most previous positive findings were not supported by subsequent studies, DRD1 and IMPA2 have been implicated in follow-up studies. Several candidate genes in the circadian rhythm pathway, BmaL1, TIMELESS, and PERIOD3, are reported to be associated with bipolar disorder. Linkage studies show many new linkage loci. In depression, the previously reported positive finding of a gene-environmental interaction between HTTLPR (insertion/deletion polymorphism in the promoter of a serotonin transporter) and stress was not replicated. Although the role of the TPH2 mutation in depression had drawn attention previously, this has not been replicated either. Pharmacogenetic studies show a relationship between antidepressant response and HTR2A or FKBP5. New technologies for comprehensive genomic analysis have already been applied. HTTLPR and BDNF promoter polymorphisms are now found to be more complex than previously thought, and previous papers on these polymorphisms should be treated with caution. Finally, this report addresses some possible causes for the lack of replication in this field.
DDB (1993)

In this paper we present an object oriented data model for VLSI/CAD data. A design data manager (DDB) based on such a model has been implemented under the UNIX/C++ environment. It has been used by a set of diverse VLSI/CAD applications of our organization. Benchmarks have shown it to perform better as compared to commercial object oriented database systems. In conjunction with the ease of data access, the data manger served to improve software productivity and a modular program architecture for our CAD system.
Early assessment of molecular progression and response by whole-genome circulating tumor DNA in advanced solid tumors (2019)

Abstract Treatment response assessment for patients with advanced solid tumors is complex and existing methods require greater precision. Current guidelines rely on imaging, which has known limitations, including the time required to show a deterministic change in target lesions. Serial changes in whole-genome (WG) circulating tumor DNA (ctDNA) were used to assess response or resistance to treatment early in the treatment course. 96 patients with advanced cancer were prospectively enrolled (91 analyzed and 5 excluded), and blood was collected before and after initiation of a new, systemic treatment. Plasma cell-free DNA libraries were prepared for either WG or WG bisulfite sequencing. Longitudinal changes in the fraction of ctDNA were quantified to retrospectively identify molecular progression (MP) or major molecular response (MMR). Study endpoints were concordance with first follow-up imaging (FFUI) and stratification of progression-free survival (PFS) and overall survival (OS). Patients with MP (n=13) had shorter PFS (median 62d vs. 310d) and OS (255d vs. not reached). Sensitivity for MP to identify clinical progression was 54% and specificity was 100%. MP calls were from samples taken a median of 28d into treatment and 39d before FFUI. Patients with MMR (n=27) had longer PFS and OS compared to those with neither call (n=51). Molecular response assessment can potentially enable early switching to potentially effective therapies, therefore minimizing side effects and costs associated with additional cycles of ineffective treatment. MMR may present a novel endpoint to target to improve long-term patient outcomes.
Why students do not turn on their video cameras during online classes and an equitable and inclusive plan to encourage them to do so (2021)

Enrollment in courses taught remotely in higher education has been on the rise, with a recent surge in response to a global pandemic. While adapting this form of teaching, instructors familiar with traditional face-to-face methods are now met with a new set of challenges, including students not turning on their cameras during synchronous class meetings held via videoconferencing. After transitioning to emergency remote instruction in response to the COVID-19 pandemic, our introductory biology course shifted all in-person laboratory sections into synchronous class meetings held via the Zoom videoconferencing program. Out of consideration for students, we established a policy that video camera use during class was optional, but encouraged. However, by the end of the semester, several of our instructors and students reported lower than desired camera use that diminished the educational experience. We surveyed students to better understand why they did not turn on their cameras. We confirmed several predicted reasons including the most frequently reported: being concerned about personal appearance. Other reasons included being concerned about other people and the physical location being seen in the background and having a weak internet connection, all of which our exploratory analyses suggest may disproportionately influence underrepresented minorities. Additionally, some students revealed to us that social norms also play a role in camera use. This information was used to develop strategies to encourage-without requiring-camera use while promoting equity and inclusion. Broadly, these strategies are to not require camera use, explicitly encourage usage while establishing norms, address potential distractions, engage students with active learning, and understand your students' challenges through surveys. While the demographics and needs of students vary by course and institution, our recommendations will likely be directly helpful to many instructors and also serve as a model for gathering data to develop strategies more tailored for other student populations.
Network (In)Security Through {IP} Packet Filtering (1992)

Entomophagous arthropods can provide valuable biological control services, but they need to fulfill their life cycle in agricultural landscapes often dominated by ephemeral and disturbed habitats. In this environment, movement is critical to escape from disturbances and to find resources scattered in space and time. Despite considerable research effort in documenting species movement and spatial distribution patterns, the quantification of arthropod movement has been hampered by their small size and the variety of modes of movement that can result in redistribution at different spatial scales. In addition, insight into how movement influences in-field population processes and the associated biocontrol services is limited because emigration and immigration are often confounded with local-scale population processes. More detailed measurements of the habitat functionality and movement processes are needed to better understand the interactions between species movement traits, disturbances, the landscape context, and the potential for entomophagous arthropods to suppress economically important pests.
Visibility in bad weather from a single image (2008)

Bad weather, such as fog and haze, can significantly degrade the visibility of a scene. Optically, this is due to the substantial presence of particles in the atmosphere that absorb and scatter light. In computer vision, the absorption and scattering processes are commonly modeled by a linear combination of the direct attenuation and the airlight. Based on this model, a few methods have been proposed, and most of them require multiple input images of a scene, which have either different degrees of polarization or different atmospheric conditions. This requirement is the main drawback of these methods, since in many situations, it is difficult to be fulfilled. To resolve the problem, we introduce an automated method that only requires a single input image. This method is based on two basic observations: first, images with enhanced visibility (or clear-day images) have more contrast than images plagued by bad weather; second, airlight whose variation mainly depends on the distance of objects to the viewer, tends to be smooth. Relying on these two observations, we develop a cost function in the framework of Markov random fields, which can be efficiently optimized by various techniques, such as graph-cuts or belief propagation. The method does not require the geometrical information of the input image, and is applicable for both color and gray images.
Handbook of Photochemistry (2006)

Since the publication of the second edition of this handbook in 1993, the field of photochemical sciences has continued to expand across several disciplines including organic, inorganic, physical, analytical, and biological chemistries, and, most recently, nanosciences. Emphasizing the important role light-induced processes play in all of these fie
Large Photoresponse in Amorphous In–Ga–Zn–O and Origin of Reversible and Slow Decay (2010)

Photoresponses of an amorphous oxide semiconductor, In–Ga–Zn–O (a-IGZO), are investigated by continuous-wave photocurrent measurements, which are discussed in terms of mobility–lifetime products . It shows that a-IGZO has ημτ values larger than those of amorphous silicon, which originate from high Fermi levels as well as long photocarrier lifetime. Reversible and very slow photocurrent decays are observed with time constants and associated activation energies . A metastable donor model and a photoreduction model are proposed to explain it. These results provide fundamental physical data for optoelectronic applications of a-IGZO.
Investigation of sequence isomer effects in AB-polybenzimidazole polymers (2013)

In the present work, a unique series of random polybenzimidazole (PBI) copolymers consisting of the recently reported novel isomeric AB-PBI (i-AB-PBI) and the well known AB-PBI were synthesized. The i-AB-PBI incorporates additional linkages (2,2 and 5,5) in the benzimidazole sequence when compared with AB-PBI. Random copolymers, varying in composition at 10 mol % increments, were synthesized to evaluate the effects of sequence isomerism in the polymer main chain without altering the fundamental chemical composition or functionality of a polymer chain consisting of 2,5-benzimidazole units. Polymer solutions were prepared in polyphosphoric acid (PPA) and cast into membranes using the sol–gel PPA process. The resulting polymers were found to have high inherent viscosities (>2.0 dL/g) and showed elevated membrane proton conductivities (∼0.2 S/cm) under anhydrous conditions at 180 °C. Fuel cell performance evaluations were conducted, and an average output voltage ranging from 0.5 to 0.60 V at 0.2 A/cm2 was observed for hydrogen/air at an operational temperature of 180 °C without applied backpressure or humidification. Herein, we report for the first time glass transition (Tg) temperatures for AB-PBI, i-AB-PBI, and an anomalous Tg effect for the series of randomized PBIs. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014, 52, 619–628
SoC Issues for RF Smart Dust (2006)

Wireless sensor nodes are autonomous devices incorporating sensing, power, computation, and communication into one system. Applications for large scale networks of these nodes are presented in the context of their impact on the hardware design. The demand for low unit cost and multiyear lifetimes, combined with progress in CMOS and MEMS processing, are driving development of SoC solutions for sensor nodes at the cubic centimeter scale with a minimum number of off-chip components. Here, the feasibility of a complete, cubic millimeter scale, single-chip sensor node is explored by examining practical limits on process integration and energetic cost of short-range RF communication. Autonomous cubic millimeter nodes appear within reach, but process complexity and substantial sacrifices in performance involved with a true single-chip solution establish a tradeoff between integration and assembly.
A novel MMI-MI SOI temperature sensor (2002)

We further develop a novel multimode-interference Michelson interferometer (MMI-MI) temperature sensor based on integrated optics technology. The sensor is made of a multimode interference coupler for achieving a Michelson interferometer (MI) sensor on a silicon-on-insulator (SOI) wafer. SOI technology shows great potential for monolithic complementary metal-oxide semiconductor (CMOS) high-speed opto-electronic devices. The MMI-MI SOI temperature sensor we designed can also reduce the sensor size and be embedded in a monolithic integrated opto-electronic circuit.
ChemInform Abstract: NMR Study of Desmotropy in Irbesartan (I), a Tetrazole‐Containing Pharmaceutical Compound. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A General Copper‐Mediated Nucleophilic 18F Fluorination of Arenes (2014)

Molecules labeled with fluorine-18 are used as radiotracers for positron emission tomography. An important challenge is the labeling of arenes not amenable to aromatic nucleophilic substitution (SNAr) with [(18)F]F(-). In the ideal case, the (18)F fluorination of these substrates would be performed through reaction of [(18)F]KF with shelf-stable readily available precursors using a broadly applicable method suitable for automation. Herein, we describe the realization of these requirements with the production of (18)F arenes from pinacol-derived aryl boronic esters (arylBPin) upon treatment with [(18)F]KF/K222 and [Cu(OTf)2(py)4] (OTf = trifluoromethanesulfonate, py = pyridine). This method tolerates electron-poor and electron-rich arenes and various functional groups, and allows access to 6-[(18)F]fluoro-L-DOPA, 6-[(18)F]fluoro-m-tyrosine, and the translocator protein (TSPO) PET ligand [(18)F]DAA1106.
Outcomes of Patients with Muscle-Invasive (pT2) Bladder Cancer According to Treatment Modalities (2006)

OBJECTIVE: To review and analyze our experience in treating patients with muscle-invasive (pT2) bladder cancer and define the proper strategies for individual patients in clinical practice.
MATERIALS AND METHODS: Totally, 61 patients were enrolled in this study from 1995 to 2000 with a male-to-female ratio of 43 to 18 and mean age of 62.4 (range, 43~83) years. Each patient's treatment and clinical course, including disease recurrence and disease-specific mortality, were retrospectively reviewed from the charts.
RESULTS: Twenty-nine patients (48%) had pathological stage pT2a TCC, and 32 patients (52%) had stage pT2b. Thirty-one patients underwent either transurethral resection of the bladder tumor alone or combined with intravesical bacillus Calmette Guerin (BCG) therapy; 21 patients underwent either radical surgery alone or combined with adjuvant chemoradiotherapy postoperatively; 2 patients received a partial cystectomy; and 7 patients received chemoradiation (MVAC/CMV or cisplatin/5FU). Five 5 patients had recurrent disease after conservative surgery for pT2a TCC leading to a radical cystectomy in I during the latter course of the disease due to progression, a partial cystectomy in 1, and secondary BCG therapy in 3. No patients died of cancer during follow-up in the pT2a group. Among the 32 patients who had pT2b TCC, 5 had recurrence after conservative surgery. Two were converted to radical surgery after failure of the chemoradiation trial, I received therapeutic radiation therapy, and 2 were under conservative treatment due to their poor general condition.
CONCLUSIONS: Tumor invasiveness and grading are 2 important parameters to consider in deciding on a bladder-sparing approach for patients with muscle-invasive bladder cancer.
Characterization of Granulations of Calcium and Apatite in Serum as Pleomorphic Mineralo-Protein Complexes and as Precursors of Putative Nanobacteria (2009)

Calcium and apatite granulations are demonstrated here to form in both human and fetal bovine serum in response to the simple addition of either calcium or phosphate, or a combination of both. These granulations are shown to represent precipitating complexes of protein and hydroxyapatite (HAP) that display marked pleomorphism, appearing as round, laminated particles, spindles, and films. These same complexes can be found in normal untreated serum, albeit at much lower amounts, and appear to result from the progressive binding of serum proteins with apatite until reaching saturation, upon which the mineralo-protein complexes precipitate. Chemically and morphologically, these complexes are virtually identical to the so-called nanobacteria (NB) implicated in numerous diseases and considered unusual for their small size, pleomorphism, and the presence of HAP. Like NB, serum granulations can seed particles upon transfer to serum-free medium, and their main protein constituents include albumin, complement components 3 and 4A, fetuin-A, and apolipoproteins A1 and B100, as well as other calcium and apatite binding proteins found in the serum. However, these serum mineralo-protein complexes are formed from the direct chemical binding of inorganic and organic phases, bypassing the need for any biological processes, including the long cultivation in cell culture conditions deemed necessary for the demonstration of NB. Thus, these serum granulations may result from physiologically inherent processes that become amplified with calcium phosphate loading or when subjected to culturing in medium. They may be viewed as simple mineralo-protein complexes formed from the deployment of calcification-inhibitory pathways used by the body to cope with excess calcium phosphate so as to prevent unwarranted calcification. Rather than representing novel pathophysiological mechanisms or exotic lifeforms, these results indicate that the entities described earlier as NB most likely originate from calcium and apatite binding factors in the serum, presumably calcification inhibitors, that upon saturation, form seeds for HAP deposition and growth. These calcium granulations are similar to those found in organisms throughout nature and may represent the products of more general calcium regulation pathways involved in the control of calcium storage, retrieval, tissue deposition, and disposal.
Methicillin-resistant staphylococci (1988)

Strains of staphylococci resistant to methicillin were identified immediately after introduction of this drug. Methicillin-resistant strains have unusual properties, the most notable of which is extreme variability in expression of the resistance trait. The conditions associated with this heterogeneous expression of resistance are described. Methicillin resistance is associated with production of a unique penicillin-binding protein (PBP), 2a, which is bound and inactivated only at high concentrations of beta-lactam antibiotics. PBP2a appears to be encoded by the mec determinant, which also is unique to methicillin-resistant strains. The relationships between PBP2a and expression of resistance and implications for the mechanism of resistance are discussed. The heterogeneous expression of methicillin resistance by staphylococci poses problems in the detection of resistant strains. Experience with several susceptibility test methods is reviewed and guidelines for performance of these tests are given. Treatment of infections caused by methicillin-resistant staphylococci is discussed. Vancomycin is the treatment of choice. Alternatives have been few because methicillin-resistant strains often are resistant to multiple antibiotics in addition to beta-lactam antibiotics. New agents which are active against methicillin-resistant staphylococci are becoming available, and their potential role in treatment is discussed.