gebhart/patrepeval huggingface dataset:
Impact of 68Ga-PSMA-11 PET/CT on Staging and Management of Prostate Cancer Patients in Various Clinical Settings: A Prospective Single-Center Study (2020)

The impact of prostate-specific membrane antigen (PSMA) PET/CT on management of prostate cancer (PCa) patients with biochemical recurrence (BCR) is well established. However, whether and how PSMA PET/CT affects the management of patients undergoing scans for other clinical indications remains unknown. The goal of this study was to determine the impact of <sup>68</sup>Ga-PSMA-11 PET/CT on initial and subsequent management decisions in a cohort of PCa patients referred for various indications (i.e., a basket trial) excluding the 2 main classic indications: BCR and presurgical staging. <b>Methods:</b> This was a prospective study of 197 patients that aimed to determine the impact of <sup>68</sup>Ga-PSMA-11 PET/CT on PCa stage and management. The indications for PSMA PET/CT were initial staging of nonsurgical candidates (30 patients) and restaging after definitive treatment (167 patients). The restaging cohort comprised patients restaged with known advanced metastatic disease (<i>n</i> = 103), after androgen deprivation therapy only (<i>n</i> = 16), after surgery and with serum prostate-specific antigen levels lower than 0.2 ng/mL (<i>n</i> = 13), after radiation therapy and not meeting the Phoenix criteria (<i>n</i> = 22), and after other primary local treatments (i.e., high-intensity focused ultrasound, focal laser ablation, cryoablation, hyperthermia, or irreversible electroporation) (<i>n</i> = 13). Patients with BCR and candidates for curative surgery were excluded. Impact on management was assessed using pre- and post-PET questionnaires completed by referring physicians, electronic chart review, or patient telephone calls. <b>Results:</b> PSMA PET/CT changed the disease stage in 135 of 197 (69%) patients (upstaging in 38%, downstaging in 30%, and no change in stage in 32%). Management was affected in 104 of 182 (57%) patients. Specifically, PSMA PET/CT impacted the management of patients who were restaged after radiation therapy without meeting the Phoenix criteria for BCR, after other definitive local treatments, and with advanced metastatic disease in 13 of 18 (72%), 8 of 12 (67%), and 59 of 96 (61%), respectively. <b>Conclusion:</b> PSMA PET/CT has a profound impact on stage and management of PCa patients outside the 2 main classic indications (BCR and presurgical staging) across all examined clinical scenarios.
Abstract 2623: Identification of neo-antigens driving melanoma response to immune checkpoint blockers via in vivo screening (2017)

Abstract Immune checkpoint blockers (ICBs) have rendered unprecedented, durable responses in metastatic melanoma, but the heterogeneous response among patients continues to be the major obstacle for their therapeutic development. It is generally hypothesized that neoantigens derived from mutated genes are involved in tumor response to ICBs, since the latter is correlated witt mutational loads of tumors. However, direct experimental evidence showing that threshold quantity or specific properties of neoantigens drive ICB response are mostly lacking. To identify and characterize neoantigens implicated in ICB response, we have generated two UV-induced melanoma models based on the BrafV600E/Pten-knockout (Braf/PKO) and Hgf-transgenic (Hgf-tg) mouse, which displayed intrinsic resistance and high sensitivity to an anti-CTLA-4 antibody, respectively. Exome sequencing identified 216 and 291 non-synonymous mutations in the Braf/PKO and UV-Hgf melanoma cell lines, respectively. By RNA sequencing, 74 (34%) and 121 (42%) of these mutated genes were found to be expressed in each model, respectively, and there were no overlapping mutations between them. The mutations found in the “sensitive” UV-Hgf melanoma were analyzed in silico for their binding affinity to MHC-I and/or MHC-II, thus characterizing putative neoantigens. A “neo-epitope” library was generated by cloning the DNA sequences flanking non-synonymous mutations in frame with the eGFP gene in a lentiviral vector. We further showed that such eGFP-fused epitopes can be presented by the cells to induce specific T cell responses. The library will be transduced into the “resistant” Braf/PKO melanoma, which will be treated with anti-CTLA-4 in mice to identify the neoantigens required for the response. To prevent immunity against eGFP expressed by tumors, the library-transduced melanoma cells will be transplanted into the eGFP-tolerant “glowing head mice”. The results will be used to determine if one, or more, of our candidate neo-epitopes can induce a response to anti-CTLA-4. We will also analyze if the response to this ICB is an epitope-specific reaction or require multiple epitopes, which will help to identify resistance mechanisms. We anticipate that our results will provide insight into the role of neoantigens in ICB response. Moreover, our models will serve as a platform to study the specific contribution and predictive value of neoantigens for melanoma response to immunotherapy, which could help improve therapeutic strategies involving ICBs. Citation Format: Chi-Ping Day, Eva Perez-Guijarro, Rajaa El Meskini, Zoe Weaver Ohler, Maxwell Lee, Howard Yang, Suman Vodnala, Shyam Sharan, Glenn Merlino. Identification of neo-antigens driving melanoma response to immune checkpoint blockers via in vivo screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2623. doi:10.1158/1538-7445.AM2017-2623
Modelling Elastic Wave Propagation In Thin Plates (2006)

Publication in the conference proceedings of EUSIPCO, Florence, Italy, 2006
On the mechanism of methanol photooxidation to methylformate and carbon dioxide on TiO2: an operando-FTIR study (2015)

This work is a mechanistic study of total and partial methanol photooxidation using operando FTIR coupled to gas phase analysis techniques (gas-IR and MS). Methoxy and formate/formyl species play a key role in the reaction. Methoxy species are formed by thermal and photochemical dissociation of methanol. The formation of methylformate is favored by a high surface coverage by methoxy species. Surface and/or bridged oxygen atoms are also important actors. Steady State Isotopic Transient Kinetic Analysis (SSITKA) experiments showed that the limiting step is the conversion of chemisorbed formyl/formate and that methylformate is a secondary product from a reaction between methoxy and neighboring formyl species. Methanol concentration, among other reaction parameters, influences greatly the selectivity of photooxidation.
Interaction of Chemical Pesticides and Their Formulation Ingredients with Microbes Associated with Plants and Plant Pests (2018)

Chemical pesticides and their formulation ingredients can have unintended effects on microbes associated with plants and plant pests. These effects can be due to direct effects on the microbes or to effects on crops or weeds that subsequently affect the microbes. In addition to fungicides, some insecticides, herbicides, and formulation compounds are toxic to plant pathogenic microbes, as well as to potentially beneficial microbes, such as those that infect insect pests. These chemicals, especially herbicides, can also indirectly affect microbes through their effects on crops and weeds. For example, glyphosate strongly impairs shikimic acid pathway-based plant defenses to microbial diseases in glyphosate-susceptible plants, significantly increasing its efficacy as an herbicide. Some herbicides induce plant defenses against plant pathogens. For a complete understanding of integrated pest management and overall cost/benefit of pesticide use, much more information is needed on microbial/pesticide interactions.
Supplementary Figure 7 from Implication of Metastasis Suppressor <i>NM23-H1</i> in Maintaining Adherens Junctions and Limiting the Invasive Potential of Human Cancer Cells (2023)

Supplementary Figure 7 from Implication of Metastasis Suppressor &lt;i&gt;NM23-H1&lt;/i&gt; in Maintaining Adherens Junctions and Limiting the Invasive Potential of Human Cancer Cells
Mesenchymal stem cell-derived interleukin-28 drives the selection of apoptosis resistant bone metastatic prostate cancer (2021)

Bone metastatic prostate cancer (PCa) promotes mesenchymal stem cell (MSC) recruitment and their differentiation into osteoblasts. However, the effects of bone-marrow derived MSCs on PCa cells are less explored. Here, we report MSC-derived interleukin-28 (IL-28) triggers prostate cancer cell apoptosis via IL-28 receptor alpha (IL-28Rα)-STAT1 signaling. However, chronic exposure to MSCs drives the selection of prostate cancer cells that are resistant to IL-28-induced apoptosis and therapeutics such as docetaxel. Further, MSC-selected/IL-28-resistant prostate cancer cells grow at accelerated rates in bone. Acquired resistance to apoptosis is PCa cell intrinsic, and is associated with a shift in IL-28Rα signaling via STAT1 to STAT3. Notably, STAT3 ablation or inhibition impairs MSC-selected prostate cancer cell growth and survival. Thus, bone marrow MSCs drive the emergence of therapy-resistant bone metastatic prostate cancer yet this can be disabled by targeting STAT3.
Herpes Zoster in rheumatoid arthritis patients receiving tofacitinib, a single center experience from Taiwan (2020)

In clinical trials of tofacitinib for rheumatoid arthritis (RA), Japanese and Korean patients had higher incidence of herpes zoster (HZ) than subjects from elsewhere; however, post-market data from Asia are lacking. Hence, we investigated the incidence of HZ and its risk factors in Taiwanese RA patients receiving tofacitinib. At a medical center in Taichung, Taiwan, we enrolled patients with active RA treated with tofacitinib between January 4, 2015 and December 9, 2017, following unsuccessful methotrexate therapy and no tofacitinib exposure RA patients as a control group. Demographic characteristics, interferon-gamma levels, and lymphocyte counts were compared. Among 125 tofacitinib-treated RA patients, 7 developed HZ, an incidence rate of 3.6/100 person-years. Patients with HZ had shorter disease duration than those without, but higher frequency of prior HZ. Baseline interferon-gamma levels and HLA-DR activated T cell counts were positively correlated and significantly lower in patients with HZ than without. Strikingly, 5/7 HZ cases occurred within 4 months of starting tofacitinib therapy. Incidence of HZ in tofacitinib-treated Taiwanese RA patients is lower than rates in Japan or Korea, and commensurate with the global average. HZ may occur soon after commencing tofacitinib therapy. The role of interferon-gamma and activated T cells in tofacitinib-related HZ deserves further investigation.
Circadian and sleep/wake-dependent variations in tau phosphorylation are driven by temperature (2019)

Taken together, our results demonstrate that tau phosphorylation follows a circadian rhythm driven mostly by body temperature and sleep, and provide the physiological basis for further understanding how sleep deregulation can affect tau and ultimately AD pathology.
Role of Inducible Nitric Oxide Synthase in Endotoxin-induced Acute Lung Injury (1998)

The role of nitric oxide (NO) in lung injury remains unclear. Both beneficial and detrimental roles have been proposed. In this study, we used mutant mice lacking the inducible nitric oxide synthase (iNOS) to assess the role of this isoform in sepsis-associated lung injury. Wild-type and iNOS knockout mice were injected with either saline or Escherichia coli endotoxin (LPS) 25 mg/kg and killed 6, 12, and 24 h later. Lung injury was evaluated by measuring lactate dehydrogenase activity in the bronchoalveolar lavage, pulmonary wet/dry ratio, and immunostaining for nitrotyrosine formation. In the wild-type mice, LPS injection elicited more than a 3-fold rise in lactate dehydrogenase activity, a significant rise in lung wet/dry ratio and extensive nitrotyrosine staining in large airway and alveolar epithelium, macrophages, and pulmonary vascular cells. This was accompanied by induction of iNOS protein and increased lung nitric oxide synthase activity. By comparison, LPS injection in iNOS knockout mice elicited no iNOS induction and no significant changes in lung NOS activity, lactate dehydrogenase activity, lung wet/dry ratio, or pulmonary nitrotyrosine staining. These results indicate that mice deficient in iNOS gene are more resistant to LPS-induced acute lung injury than are wild-type mice.
Efficient Recovery Strategies for IP/MPLS over Transport Networks<sup>1</sup> (2006)

Three recovery mechanisms are implemented with the end-to-end signaling capabilities The results presenting the network equipment interface requirements and recovery time performance confirm the advantages of cross-layer coordination of the IP/MPLS data client networks served by a GMPLS transport network
Antiproton Dispersion in Magnetically Insulated Inertial Confinement Fusion Propulsion (2005)

A propulsion system based on magnetically insulated inertial confinement fusion and using antiprotons to produce intense magnetic fields, could open the solar system to trade and settlement. The magnetic fields created at the antiproton beam focal point can be quite intense, as high as 24 MG, trapping fusion fuels and triggering a fu sion reaction that propagates throughout a pellet. As the antiprotons are injected into pellet the developing plasma will disperse the antiproton beam, and defocus the beam, thereby decreasing transient confining magnetic fields. An analysis of the coupl ing of the developing plasma and the induced transient magnetic fields, demonstrates that proper tuning of the antiproton beam energy will result in the annihilation of the mass over a negligible depth with very little beam spreading. Hence, it will be po ssible to ignite a fusion reaction using antiprotons, resulting in rockets with a specific impulse exceeding 100,000 seconds at high thrust to mass ratios.
Seawater Based Fracturing Fluid: A Game Changer in Hydraulic Fracturing Applications in Saudi Arabia (2017)

Abstract Hydraulic fracturing activities in tight gas wells in Saudi Arabia have been exponentially increasing to meet domestic demand for natural gas. During each fracturing stage, up to 125,000 gallons of groundwater is currently being used. The need to reduce groundwater usage during fracturing treatments has been set as a priority, and alternative water sources for fracturing applications that can significantly reduce groundwater usage have been intensively explored. One such alternative water source is seawater as a base fluid for hydraulic fracturing. The primary challenge for this application is the tendency for scale precipitation due to the high sulfate content in seawater and its potential incompatibility with formation water. Without proper prevention and mitigation measures, this scale precipitation can induce formation damage and reduce the fracture conductivity. To minimize scaling tendencies, an in-house multidisciplinary team has performed extensive collaborative research to identify a scale inhibitor appropriate for Arabian Gulf seawater and formation water. Scale precipitation can be further mitigated by filtering the seawater with a nanofiltration system to dramatically reduce the sulfate ion as well as lower the calcium and magnesium ions. The successful application of seawater-based fracturing fluid in Saudi Arabia opens up the door to minimizing consumption of groundwater in hydraulic fracturing operations. Millions of gallons of groundwater could be saved and development of sustainable water resources could be achieved. This paper will describe the optimization of a scale inhibitor and fracturing fluid system, the selection of the nanofiltration system, and the first field applications of the seawater based fracturing fluid system in high-temperature gas wells in Saudi Arabia.
Process Development of a Potent Bradykinin 1 Antagonist (2009)

As part of Merck’s continued research effort on inflammation and pain, a safe synthesis of an orally bioavailable and CNS penetrant bradykinin 1 antagonist was developed and demonstrated on kilogram scale. The key step included a novel regioselective metal−halogen exchange reaction on 1,2-dibromo-5-chloro-3-fluorobenzene using isopropyl magnesium chloride to install the 1,2,4-oxadiazole ring structure. Suzuki cross-coupling reaction between a highly functionalized and sterically hindered electrophile and boronic ester generated the biaryl ring system, which was converted to the target molecule (1) using standard chemistry. The safe installation of a 1,2,4-oxadiazole ring proved to be challenging since the original synthetic route relied on the preparation of a highly functionalized benzonitrile using potassium cyanide and resulted in low yields and large amounts of potentially hazardous waste. Overall, a safe and robust synthesis was developed, which occurred in eight linear steps with an overall yield of 28%.
Creep Resistance of Disk Alloy CH98 with Tungsten and Niobium Additions (2003)

Gas turbine engines for future subsonic transports will likely have higher pressure ratios which will require nickel-base superalloy disks with temperature capability up to 1400 F, an increase of about 200 F over current engines. Several advanced disk alloys are being developed to fill this need. One of these, CH98, is a promising candidate for gas turbine engines and is being studied in NASA's AST Program. Additions of the refractory elements tungsten and niobium have been shown to improve tensile and creep properties while maintaining good high temperature fatigue crack growth resistance. Further improvements in creep and crack growth resistance can be achieved with a coarse grain microstructure. The purpose of the present study is aimed at providing a detailed assessment of 0.2 percent creep rates for coarse grain CH98 with tungsten and niobium additions over a range of temperatures and stresses of interest to disk applications.
Two-detector coincidence routing circuit for personal computer-based multichannel analyzer (1995)

A routing circuit for Oxford Instrument’s PCA II multichannel analyzer card is described. The circuit allows recording of events requiring coincident signals from two out of four detectors. As an example, the use of the routing circuit in a time-differential perturbed angular correlation spectrometer is outlined.
Prenatal Diagnosis of Loeys-Dietz Syndrome (2014)

Key words Loeys-Dietz syndrome - aortic root dilatation - fetal ultrasound - prenatal diagnosis
Energy Levels and Observed Spectral Lines of Xenon, Xe I through Xe LIV (2004)

The energy levels and observed spectral lines of the xenon atom, in all stages of ionization for which experimental data are available, have been compiled. Sufficient data were found to generate level and line tables for Xe I–Xe XI, Xe XIX, Xe XXV–Xe XXIX, Xe XLIII–Xe XLV, and Xe LI–Xe LIV. For Xe LIII and Xe LIV theoretical values are compiled for the energy levels. In 15 of the other stages a few lines are reported. Experimental g factors are included for Xe I, Xe II, and Xe III. A value, either experimental, semiempirical, or theoretical, is included for the ionization energy of each ion.
The effect of rebamipide on Helicobacter pylori extract‐mediated changes of gene expression in gastric epithelial cells (2003)

These findings suggest that rebamipide could inhibit inflammatory reactions and tumour progression by modifying H. pylori infection-induced gene expression in gastric epithelial cells.
Guidelines for the management of HIV infection in pregnant women and the prevention of mother‐to‐child transmission of HIV (2005)

transmission – background The prevalence of HIV infection amongst women giving birth in England and Wales has increased every year since 1990. Results from the Unlinked Anonymous Surveys of HIV infection in pregnancy, show that in 2003, the prevalence reached one in 180 (0.56%) in inner London, one in 271 in outer London (0.37%) and one in 1282 (0.08%) in the rest of England [1]. The majority of these women are from sub-Saharan Africa. The Department of Health policy of recommending an HIV test to every pregnant woman [2] has resulted in an increase in the proportion of these women who are aware of their diagnosis prior to delivery (more than 80 % in London in 2001) and a decrease in the absolute number of infants infected in the UK [3]. In untreated women the risk of transmission is related to maternal health, obstetric factors and infant prematurity. Overall there is a close linear correlation between maternal viral load and risk of transmission but rare transmissions have been reported even at plasma viraemia less than 400 RNA copies/mL [4]. CD4 counts and clinical disease stage have been shown in some cohorts to have an association with the risk of transmission even after controlling for viral load. The only obstetric factors that consistently show an association with risk of transmission are mode of delivery and duration of membrane rupture, but invasive procedures in labour are generally avoided as they pose a theoretical risk of iatrogenic transmission. Delivery before 34 weeks of gestation has been shown to be associated with an increased risk of transmission. There are still relatively few, and often conflicting data, on the safety of antiretroviral therapy (ART) in pregnancy, and the management of any HIV-positive pregnant woman
The Cyclic Hardening of Copper Single Crystals (1969)

Copper single crystals hardened by cyclic straining at low amplitude have been sectioned parallel to and perpendicular to the primary slip-plane. The detailed dislocation arrangements were determined by transmission electron microscopy and the surface slip behaviour observed by optical replica techniques. The results indicate that the hardening process is caused predominantly by the accumulation of dislocation debris in the form of complex braids of dipoles and monopoles and that it exhibits numerous features similar to Stage-I unidirectional hardening. These microstructural observations provide a rationale for many of the properties of cyclically hardened materials.
Antiproliferative effects of Camellia sinensis, Frangula alnus and Rosmarinus officinalis (2013)

The use of medicinal plants is becoming increasingly appreciated in suppressing cancer growth and cancer prevention. In this study the antiproliferative effects of the water extracts of previously obtained ethanolic dry extracts of three different medicinal plants (Camellia sinensis, Frangula alnus from two different places and Rosmarinus officinalis) using cell lines derived from human cervix adenocarcinoma (Hela cells) were investigated. The extract of Camellia sinensis exhibited significant cytotoxic effect against Hela cells (IC50 40.88 ?g/ml). Screening in Hela cells revealed a moderate cytotoxic effect (IC50 80.26?g/ml) of the extract of Rosmarinus officinalis, a mild cytotoxic effect (IC50 148.05 ?g/ml) of the extract of Frangula alnus (originating in Bosnia), and the extract of Frangula alnus (originating in Serbia) did not show active cytotoxicity (IC50 &gt; 200 ?g/ml). The best antiproliferative properties are those of Camellia sinensis, followed by Rosmarinus officinalis, and the least effective was Frangula alnus. As regards geographic origin, the Frangula alnus from Bosnia possessed better antiproliferative effects than Frangula alnus from Serbia.