gebhart/patrepeval huggingface dataset:
Data from Multi-center, Placebo-controlled, Double-blind, Randomized Study of Oral Toceranib Phosphate (SU11654), a Receptor Tyrosine Kinase Inhibitor, for the Treatment of Dogs with Recurrent (Either Local or Distant) Mast Cell Tumor Following Surgical Excision (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; The purpose of this study was to determine the objective response rate (ORR) following treatment of canine mast cell tumors (MCT) with toceranib phosphate (Palladia, SU11654), a kinase inhibitor with both antitumor and antiangiogenic activity through inhibition of KIT, vascular endothelial growth factor receptor 2, and PDGFRβ. Secondary objectives were to determine biological response rate, time to tumor progression, duration of objective response, health-related quality of life, and safety of Palladia.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Dogs were randomized to receive oral Palladia 3.25 mg/kg or placebo every other day for 6 weeks in the blinded phase. Thereafter, eligible dogs received open-label Palladia.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; The blinded phase ORR in Palladia-treated dogs (&lt;i&gt;n&lt;/i&gt; = 86) was 37.2% (7 complete response, 25 partial response) versus 7.9% (5 partial response) in placebo-treated dogs (&lt;i&gt;n&lt;/i&gt; = 63; &lt;i&gt;P&lt;/i&gt; = 0.0004). Of 58 dogs that received Palladia following placebo-escape, 41.4% (8 complete response, 16 partial response) experienced objective response. The ORR for all 145 dogs receiving Palladia was 42.8% (21 complete response, 41 partial response); among the 62 responders, the median duration of objective response and time to tumor progression was 12.0 weeks and 18.1 weeks, respectively. Palladia-treated responders scored higher on health-related quality of life versus Palladia-treated nonresponders (&lt;i&gt;P&lt;/i&gt; = 0.030). There was no significant difference in the number of dogs with grade 3/4 (of 4) adverse events; adverse events were generally manageable with dose modification and/or supportive care.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Palladia has biological activity against canine MCTs and can be administered on a continuous schedule without need for routine planned treatment breaks. This clinical trial further shows that spontaneous tumors in dogs are good models to evaluate therapeutic index of targeted therapeutics in a clinical setting.&lt;/p&gt;&lt;/div&gt;
Synthesis of calixarene–polyglycerol conjugates and their self-assembly toward nano and microtubes (2016)

The molecular self-assembly of new hyperbranched polymers and copolymers consisting of polyglycerol and citric acid with a calixarene core results in nano and microtubes with the ability of loading of curcumin as an anticancer drug.
A monoclonal antibody to common acute lymphoblastic leukemia antigen (CALLA) and its expression on several human tumor cell lines (1992)

We describe a newly-made murine monoclonal antibody to the common acute lymphoblastic leukemia antigen (CALLA), named SHB-10. The antigen detected by SHB-10 has a molecular weight of about 105 kDa. This antibody is very similar to that of conventional anti-CD10 Ab on indirect flowcytometric analysis using lymphoid malignant cell lines and peripheral lymphocytes of acute lymphoblastic leukemia (ALL) patients. The binding of anti-CD10 to Daudi cell and peripheral lymphocytes of ALL patients is blocked by SHB-10. Thus this monoclonal antibody is thought to detect the CALLA. The distribution of antigen detected by SHB-10 on several cell lines of neuroectodermal tumor and lymphoid malignancy was analysed and a slight difference in their cell surface expression is observed when compared with that by conventional anti-CD10. Further biochemical analysis is now under way for a better characterization of this antigen.
Fetal urinary tract obstruction and trisomy 18 mosaicism. A case report. (1988)

Routine ultrasound examination has led increasingly to antepartum detection of fetal anomalies. Management decisions remain difficult, however, because information on the presence of other anomalies is frequently unobtainable. A case of fetal urinary tract obstruction, although apparently an isolated defect, proved to be associated with a lethal chromosome abnormality, trisomy 18 mosaicism.
Hydrophobic Small-Molecule Polymers as High-Temperature-Resistant Inhibitors in Water-Based Drilling Fluids (2023)

Water-based drilling fluids can cause hydration of the wellbore rocks, thereby leading to instability. This study aimed to synthesize a hydrophobic small-molecule polymer (HLMP) as an inhibitor to suppress mud shale hydration. An infrared spectral method and a thermogravimetric technique were used to characterize the chemical composition of the HLMP and evaluate its heat stability. Experiments were conducted to measure the linear swelling, rolling recovery rate, and bentonite inhibition rate and evaluate accordingly the inhibition performance of the HLMP. Moreover, the HLMP was characterized through measurements of the zeta potential, particle size distribution, contact angles, and interlayer space testing. As confirmed by the results, the HLMP could successfully be synthesized with a favorable heat stability. Furthermore, favorable results were found for the inhibitory processes of the HLMP on swelling and dispersed hydration during mud shale hydration. The positively charged HLMP could be electrically neutralized with clay particles, thereby inhibiting diffusion in the double electron clay layers. The hydrophobic group in the HLMP molecular structure resulted in the formation of a hydrophobic membrane on the rock surface, enhancing the hydrophobicity of the rock. In addition, the small molecules of the HLMP could plug the spaces between the layers of bentonite crystals, thereby reducing the entry of water molecules and inhibiting shale hydration.
On the Case of the Misplaced Hydrogens (2020)

Few other elements play a more central role in biology than hydrogen. The interactions, bonding and movement of hydrogen atoms are central to biological catalysis, structure and function. Yet owing to the elusive nature of a single hydrogen atom few experimental and computational techniques can precisely determine its location. This is exemplified in short hydrogen bonds (SHBs) where the location of the hydrogen atom is indicative of the underlying strength of the bonds, which can vary from 1-5 kcal/mol in canonical hydrogen bonds, to an almost covalent nature in single-well hydrogen bonds. Owing to the often-times inferred position of hydrogen, the role of SHBs in biology has remained highly contested and debated. This has also led to discrepancies in computational, biochemical and structural studies of proteins thought to use SHBs in performing chemistry and stabilizing interactions. Herein, we discuss in detail two distinct examples, namely the conserved catalytic triad and the photoreceptor, photoactive yellow protein, where studies of these SHB-containing systems have permitted contextualization of the role these unique hydrogen bonds play in biology.
Modulation of breast cancer cell-free DNA with surgical resection. (2013)

11060 Background: Recently we demonstrated the ability to detect the presence of invasive breast cancer by next generation sequence (NGS) analysis of cell-free DNA (cfDNA) in serum without prior knowledge of the specific gene perturbations of the neoplasm (J. Clin. Oncology 2010; 28 (15S):10505). We hypothesized that cfDNA levels would hold promise as a marker to monitor therapeutic efficacy in breast cancer. In this study, we sought to determine whether cfDNA decreases after surgery in patients with operable invasive breast cancer. Methods: Serum was collected before and 1-4 weeks after surgery from 16 breast cancer patients and also from 24 age and gender matched controls. cfDNA was isolated from the serum, amplified by Chronix proprietary method and sequenced on an Illumina HiSeq platform. The breast cancer derived cfDNA sequences from each patient were compartmentalized in 250kbp bins, normalized, and compared to the mean (+/- 3SD) of the controls to identify regions of chromosomal number imbalance (CNI). Genomic DNA was isolated from the primary tumor and blood WBC buffy coat, pre-amplified, sequenced and subjected to comparative analysis with cfDNA. Results: Analysis of pre- and post surgery serum demonstrate that CNIs are present in the pre-surgery serum cfDNA that correlated with the associated tumor CNI and was not observed in WBC genomic DNA. The number of tumor associated CNI DNA biomarkers ranged from as low as 3 to as high as 865. In 13 of 16 patients (81%) analyzed, the post-surgery cfDNA was free of detectable tumor related-CNI DNA. In the remaining 3 patients, only a partial reduction in tumor specific CNI DNA serum biomarkers was observed, since some markers were still detectable after surgery. Conclusions: cfDNA from primary breast carcinomas accurately reflects tumor CNI. Removal of the primary tumor results in the elimination of tumor cfDNA in the majority of patients. Thus cfDNA may be of clinical value in evaluation of therapeutic efficacy on a real time basis. Further work is needed to determine if residual tumor CNI in cfDNA after surgery is a marker of minimal residual disease which can be pursued as a prognostic marker.
Tunable metamaterial binary nano-particle dispersed liquid crystal cells (2010)

Metamaterials with tunable properties are of great importance due to potential applications in super-resolution lensing and sensors. In this paper we study the feasibility of the fabrication of a metamaterial using binary nanoparticle-dispersed liquid crystal cell (NDLCC). Depending on the angle between the director axis of the LCC and the incident beam, types, radii, and volume filling fractions of the nanoparticles, a negative index of refraction cell is obtained in a certain range of frequencies. The effective index of refraction is calculated using the effective medium theory. The scattering, extinction, and absorption of such a NDLCC cell is also found. Finally, the influence of the various parameters to obtain such a negative index metamaterial has been investigated.
Motor endplate‐expressing cartilage‐muscle implants for reconstruction of a denervated hemilarynx (2018)

NA Laryngoscope, 129:1293-1300, 2019.
Restoration of Wadi Aquifers by Artificial Recharge with Treated Waste Water (2012)

Fresh water resources within the Kingdom of Saudi Arabia are a rare and precious commodity that must be managed within a context of integrated water management. Wadi aquifers contain a high percentage of the naturally occurring fresh groundwater in the Kingdom. This resource is currently overused and has become depleted or contaminated at many locations. One resource that could be used to restore or enhance the fresh water resources within wadi aquifers is treated municipal waste water (reclaimed water). Each year about 80 percent of the country's treated municipal waste water is discharged to waste without any beneficial use. These discharges not only represent a lost water resource, but also create a number of adverse environmental impacts, such as damage to sensitive nearshore marine environments and creation of high-salinity interior surface water areas. An investigation of the hydrogeology of wadi aquifers in Saudi Arabia revealed that these aquifers can be used to develop aquifer recharge and recovery (ARR) systems that will be able to treat the impaired-quality water, store it until needed, and allow recovery of the water for transmittal to areas in demand. Full-engineered ARR systems can be designed at high capacities within wadi aquifer systems that can operate in concert with the natural role of wadis, while providing the required functions of additional treatment, storage and recovery of reclaimed water, while reducing the need to develop additional, energy-intensive desalination to meet new water supply demands.
A Case of Fibrolamellar Hepatocellular Carcinoma where Lung Metastasis was Resected (2018)

症例は45歳，男性．検診で肝機能障害を指摘され近医を受診し，腹部超音波検査で8 cmの肝腫瘍を認め当院にて精査を行った．HBs抗原とHCV抗体は陰性でAFPとPIVKA-IIは著明に上昇し，画像検査でfibrolamellar hepatocellular carcinoma（以下，FLHCCと略記）を疑い，肝S5/6亜区域切除を施行した．病理組織学的には，索状構造をとって増殖した腫瘍胞巣が密で厚い層状の膠原線維束に取り囲まれたFLHCCに特徴的な所見であった．腫瘍マーカーが漸増し左肺上葉に増大する単発性の小結節を認め，術後22カ月に肺部分切除を施行し病理組織学的にもFLHCCの転移と診断した．現在は新たな再発を認めず，初回術後50カ月の生存を得ている．FLHCCは通常の肝細胞癌と異なる臨床病理組織学的特徴を持つ稀な原発性肝癌であり，積極的な外科切除が奏効した1例を経験したので，文献的考察を加え報告する．
ChemInform Abstract: Two Novel Antiviral Terpenoids from the Cultured Perovskia atriplicifolia. (2015)

Abstract Isolation and structural elucidation of norperovskatone (I) and biperovskatone (II) are described.
On random weights for texture generation in one layer CNNS (2017)

Recent work in the literature has shown experimentally that one can use the lower layers of a trained convolutional neural network (CNN) to model natural textures. More interestingly, it has also been experimentally shown that only one layer with random filters can also model textures although with less variability. In this paper we ask the question as to why one layer CNNs with random filters are so effective in generating textures? We theoretically show that one layer convolutional architectures (without a non-linearity) paired with the an energy function used in previous literature, can in fact preserve and modulate frequency coefficients in a manner so that random weights and pretrained weights will generate the same type of images. Based on the results of this analysis we question whether similar properties hold in the case where one uses one convolution layer with a non-linearity. We show that in the case of ReLu non-linearity there are situations where only one input will give the minimum possible energy whereas in the case of no nonlinearity, there are always infinite solutions that will give the minimum possible energy. Thus we can show that in certain situations adding a ReLu non-linearity generates less variable images.
Subcutaneous air-pouch. (2015)

&lt;p&gt;Clinical appearance of the air-pouch on the dorsum of the mouse after skin flap procedure.&lt;/p&gt;
45 GHz self-pulsation with narrow linewidth in quantum dot Fabry-Perot semiconductor lasers at 1.5 µm (2005)

Self-pulsation at 45 GHz repetition frequency has been demonstrated in 1.5 µm monolithic single-section quantum dot Fabry-Perot semiconductor lasers without saturable absorber. The mode-beating exhibits a narrow linewidth below 100 kHz, demonstrating high phase correlation between these modes. Such modelocked lasers open ways to low timing-jitter components for clock recovery or millimetre-wave generation in wireless transmission applications.
Supplemental Figure 1 from &lt;i&gt;NFE2L2&lt;/i&gt; Mutations Enhance Radioresistance in Head and Neck Cancer by Modulating Intratumoral Myeloid Cells (2023)

&lt;p&gt;Mutational landscape and details of NFE2L2 gene mutation in a cohort of oral cavity cancer patients treated with surgery and postoperative (chemo)radiotherapy at Stanford University.&lt;/p&gt;
Heterogeneous photoredox flow chemistry for the scalable organosynthesis of fine chemicals (2020)

Large-scale photochemical synthesis of high value chemicals under mild conditions is an ideal method of green chemical production. However, a scalable photocatalytic process has been barely reported due to the costly preparation, low stability of photosensitizers and critical reaction conditions required for classical photocatalysts. Here, we report the merging of flow chemistry with heterogeneous photoredox catalysis for the facile production of high value compounds in a continuous flow reactor with visible light at room temperature in air. In the flow reactor system, polymeric carbon nitrides, which are cheap, sustainable and stable heterogeneous photocatalysts, are immobilized onto glass beads and fibers, demonstrating a highly flexible construction possibility for devices of the photocatalytic materials. As an example of the production of high value chemicals, important chemical structures such as cyclobutanes, which are basic building blocks for many pharmaceutical compounds, like magnosalin, are synthesized in flow with high catalytic efficiency and stability.
Induction of Immunity to Neuroblastoma Early after Syngeneic Hematopoietic Stem Cell Transplantation Using a Novel Mouse Tumor Vaccine (2007)

Autologous HSCT has resulted in improved event-free survival in patients with advanced neuroblastoma, but most of these patients still relapse. We previously reported that transient transfection of mouse neuroblastoma cells with plasmid DNA vectors encoding immune costimulatory molecules generates cell-based vaccines capable of inducing potent antitumor T cell immunity. In this study, we explored the effectiveness of tumor vaccine administration soon after HSCT. Soon after transplantation, only vaccinated mice that had received an adoptive transfer of syngeneic T cells survived tumor challenge. Tumor protective immunity in the transplant recipients was dependent on CD4(+) and CD8(+) T cells, and tumor-reactive T cells in the spleens of vaccinated mice could be detected in IFN-gamma enzyme-linked immunosorbent spot (ELISPOT) assays. Our data indicate that the adoptive transfer of T cells was absolutely required for induction of protective immunity by the tumor vaccine. Adoptive transfer of T cells accelerated T cell reconstitution, but it also resulted in increased percentages of CD4(+)CD25(+)Foxp3(+) cells soon after HSCT. Treatment of HSC transplant recipients with an anti-CD25 mAb before tumor vaccination inhibited antitumor immunity and significantly decreased the number of IFN-gamma-secreting tumor-specific CD4 T cells. However, physical depletion of CD25(+) cells from the adoptively transferred splenocytes appeared to increase the efficacy of tumor vaccination. Collectively, these results demonstrate that anti-neuroblastoma immunity can be induced soon after HSCT using a novel cell-based cancer vaccine. However, sufficient numbers of T cells must be added to the graft to achieve protective antitumor immunity, and depletion of CD25(+) T cells from adoptively transferred T cells might provide some additional benefit. These translational studies will aid in our development of post-HSCT vaccines for neuroblastoma.
Controlling the Minimal Self Assembly of “Complex” Polyoxometalate Clusters (2014)

Despite the vast number of polyoxometalate clusters now known, an ongoing and important challenge is to understand causality in the assembly of "complex" clusters at a mechanistic level, since this is the only way the rational, targeted synthesis of new compounds will ever be achieved. Often, the complexity of the reactions themselves makes such investigations near impossible, as very small changes can often make dramatic differences. Herein, we explore a very simple [A + B] binary synthetic system that gives rise to the facile assembly of two isomeric anions, [Fe(III)(H2O)2{γ-Fe(III)SiW9O34(H2O)}2](11-) (1) and [Fe(III)(H2O)2{γ-Fe(III)2SiW8O33(H2O)2}{γ-SiW10O35}](11-) (2), which can be formed as individual and dimeric species (3) and (4). Furthermore, the simple binary nature of this synthetic system allowed its investigation by a comprehensive time-resolved ESI-MS analysis, yielding unprecedented mechanistic information regarding the initial interactions and reorganizations of the {γ-SiW10} precursor in the presence of Fe(2+).
Supplementary Fig. from Quantitative live imaging of cancer and normal cells treated with Kinesin-5 inhibitors indicates significant differences in phenotypic responses and cell fate (2023)

Supplementary Fig. from Quantitative live imaging of cancer and normal cells treated with Kinesin-5 inhibitors indicates significant differences in phenotypic responses and cell fate
Increased Fat Absorption From Enteral Formula Through an In‐line Digestive Cartridge in Patients With Cystic Fibrosis (2017)

Use of this in-line digestive cartridge was safe and well tolerated, and resulted in significantly increased levels of plasma omega-3 FA used with enteral formula, suggesting an overall increased fat absorption.
Group 4 Metallocenes Bearing η<sup>5</sup>-2-(<i>N</i>-Azolyl)indenyl Ligands: Synthesis, Structure Characterization, and Olefin Polymerization Catalysis (2009)

The Pd-catalyzed cross-coupling reactions of readily available 2-bromo-1H-indene with 1H-pyrrole, 1H-indole, 9H-carbazole, and their derivatives were shown to be convenient methods to obtain novel ligands containing azole fragments bonded with cyclopentadienyl via nitrogen. An alternative protocol using enol triflates of 1-indanone or 2-indanone is also useful, particularly for synthesizing indenes bearing the N-azolyl fragment in position 1. On the other hand, the synthesis of 2-(1H-benzimidazol-1-yl)-1H-indene can be achieved via the Cu-catalyzed reactions only. The substituted indenes with the N-azolyl fragment in position 2 were further used for obtaining several semisandwich complexes of zirconium, [η5-2-(N-azolyl)indenyl]zirconium tribromides, as well as symmetrical and unsymmetrical Waymouth-type zirconium and hafnium complexes containing indenyl ligands bearing planar N-azolyl or aryl fragments in position 2. These metallocenes were unambiguously characterized, including by X-ray crystal structure analysis, and a study of the fluxional behavior of several Waymouth-type complexes in solution was carried out by NMR spectroscopy. Finally, novel Waymouth-type complexes, after being activated by MAO, were found to form active catalysts of ethylene homopolymerization and ethylene/1-octene copolymerization.
Comparison of Primary Neuroblastoma Tumors and Derivative Early-Passage Cell Lines Using Genome-Wide Single Nucleotide Polymorphism Array Analysis (2009)

Stromal contamination is one of the major confounding factors in the analysis of solid tumor samples by single nucleotide polymorphism (SNP) arrays. As we propose to use genome-wide SNP microarray analysis as a diagnostic platform for neuroblastoma, the sensitivity, specificity, and accuracy of these studies must be optimized. To investigate the effects of stromal contamination, we derived early-passage cell lines from nine primary tumors and compared their genomic signature with that of the primary tumors using 100K SNP arrays. The average concordance between tumor and cell line for raw loss of heterozygosity (LOH) calls was 96% (range, 91-99%) and for raw copy number alterations, 71% (range, 43-87%). In general, there were a larger number of LOH events identified in the cell lines compared with the matched tumor samples (mean increase, 3.2% +/- 1.9%). We have developed an algorithm that shows that the presence of stroma contributes to under-reporting of LOH and copy number loss. Notable findings in this sample set were uniparental disomy of chromosome arms 11p, 1q, 14q, and 15q and a novel area of amplification on chromosome band 11p15. Our analysis shows that LOH was identified significantly more often in derived cell lines compared with the original tumor samples. Although these may in part be due to clonal selection during adaptation to tissue culture, our study indicates that stromal contamination may be a major contributing factor in underestimation of LOH and copy number loss events.
Temperature dependence of coercivity in MnBi (1993)

In contrast to most ferromagnetic materials, the low-temperature phase of MnBi exhibits an increased coercivity, Hc, with temperature. μ0Hc has a value of 0.2 T at room temperature, and rises dramatically to a maximum value of 1.9 T at 550 K. In the temperature region near its maximum value, Hc is much larger than that of Nd-Fe-B and has a very-low-temperature coefficient. For this reason, MnBi has a great potential as a permanent magnet material at high temperatures. To describe the temperature dependence of Hc, we develop a hybrid domain-wall pinning model which combines Hilzinger and Kronmüller’s scaling theory for an anisotropic domain wall with Gaunt’s theory of thermal activation. The hybrid model gives an excellent fit to the temperature dependence of Hc and provides good estimates for the domain-wall energy and thickness over the temperature range studied.