gebhart/patrepeval huggingface dataset:
Cell surface antigens in squamous cell carcinoma of the oral cavity (1986)

The ABH isoantigen was investigated in 80 patients with squamous cell carcinoma of the oral cavity and in their 46 affected lymph nodes. Isoantigen deletion shows a characteristic pattern of benign to malignant transformation of oral cancer. Total loss of isoantigen was found in anaplastic tumours, in metastatic lymph nodes and in the majority of advanced stage tumours. Total loss of isoantigen in metastatic lymph nodes indicates a frequent discharge of isoantigen-negative metastatic cells from the primary tumours to the lymph nodes and the regional organs. It seems that with the recent techniques a prospective observation of ABH isoantigen added to other pathological and clinical findings could be of prognostic significance in patients with squamous cell carcinoma of the oral cavity.
Population Aging and Cancer (2005)

Although malignant tumors occur at all ages, cancer disproportionately strikes individuals in the age group 65 years and older. Data from the National Cancer Institute Surveillance, Epidemiology, and End Results Program for the most recent five-year period, 1998-2002, reveal that 56% of all newly diagnosed cancer patients and 71% of cancer deaths are in this age group. Median ages of cancer patients at death for the major tumors common to both males and females, all races (lung, colorectal, lymphoma, leukemia, pancreas, stomach, urinary bladder) range from 71 to 77 years. The median age for prostate cancer is 79 years; for ovarian and female breast cancer, the median age is 71 for each tumor. These cancer statistics when cast against the demographic changes occurring in the U.S. population take on urgency and importance for cancer treatment and care in our nation's health care system. The U.S. Census Bureau demographic projections indicate that the number of persons 65 years and older in the United States will double from the current estimate of 35 million persons to a projected 70 million by 2030. Barring any cancer prevention breakthroughs, the expansion of the aged population will likely increase the absolute number of older individuals diagnosed and treated for cancer in coming decades. The United States is not unique as an aging developed industrial nation with a high proportion of the cancer burden in the elderly. Other developed industrial countries have a potentiality for increased cancer incidence and mortality as their populations grow older. This paper, using U.S. Bureau of Census demographic projections and current age standardized death rates per 100,000 population (from Worldwide Cancer Mortality Statistics, Cancer Mondial, WHO, and the International Association for Research on Cancer) compares cancer in the elderly in Italy and the United States. Italy is demographically ranked as the oldest nation in the world. Dimensions of the cancer burden challenge ahead are inferred in the context of two countries with aging populations to underscore the possible increase that demographic factors may have on the magnitude of the cancer problem for older persons in the next 25 years.
PhaseLift: Exact and Stable Signal Recovery from Magnitude Measurements via Convex Programming (2012)

Abstract Suppose we wish to recover a signal \input amssym $\font\abc=cmmib10\def\bi#1{\hbox{\abc#1}} {\bi x} \in {\Bbb C}^n$ from m intensity measurements of the form $\font\abc=cmmib10\def\bi#1{\hbox{\abc#1}} |\langle \bi x,\bi z_i \rangle|^2$ , $i = 1, 2, \ldots, m$ ; that is, from data in which phase information is missing. We prove that if the vectors $\font\abc=cmmib10\def\bi#1{\hbox{\abc#1}}{\bi z}_i$ are sampled independently and uniformly at random on the unit sphere, then the signal x can be recovered exactly (up to a global phase factor) by solving a convenient semidefinite program–‐a trace‐norm minimization problem; this holds with large probability provided that m is on the order of $n {\log n}$ , and without any assumption about the signal whatsoever. This novel result demonstrates that in some instances, the combinatorial phase retrieval problem can be solved by convex programming techniques. Finally, we also prove that our methodology is robust vis‐à‐vis additive noise. © 2012 Wiley Periodicals, Inc.
Data-Driven Response Generation in Social Media (2011)

We present a data-driven approach to generating responses to Twitter status posts, based on phrase-based Statistical Machine Translation. We find that mapping conversational stimuli onto responses is more difficult than translating between languages, due to the wider range of possible responses, the larger fraction of unaligned words/phrases, and the presence of large phrase pairs whose alignment cannot be further decomposed. After addressing these challenges, we compare approaches based on SMT and Information Retrieval in a human evaluation. We show that SMT outperforms IR on this task, and its output is preferred over actual human responses in 15 % of cases. As far as we are aware, this is the first work to investigate the use of phrase-based SMT to directly translate a linguistic stimulus into an appropriate response. 1
Location and Orientation of Homologous Sequences in the Genomes of Five Herpesviruses (1983)

Molecular hybridization experiments were carried out to investigate homologous regions in the genomes of herpes simplex virus types 1 and 2 (HSV-1 and HSV-2), equid herpesvirus 1 (EHV-1), pseudorabies virus (PRV) and varicella-zoster virus (VZV). Virion DNA probes from EHV-1, PRV and VZV hybridized to similar regions of the HSV genome, and the use of cloned DNA probes allowed heterologous genomes to be oriented with respect to homologous regions. The HSV-1 and HSV-2 genomes are colinear, the EHV-1 and VZV genomes are colinear with the IL or ISL genome arrangement of HSV, and the PRV genome is essentially colinear with the IL genome arrangement of HSV except that the region 0.1 to 0.4 fractional genome units appears to be inverted. A detailed analysis of sequences in the HSV-2 and PRV genomes to which the HSV-1 major capsid protein gene hybridized was carried out in order to demonstrate the application of molecular hybridization to the location of genes in heterologous genomes. The lesion in a DNA-positive temperature-sensitive mutant of PRV was mapped within the putative PRV major capsid protein gene. We conclude that the herpesviruses we have studied possess several highly conserved genes, and propose that they are similar in genetic organization despite presumably separate evolutionary histories.
Nonenzymatic Transformation of Amorphous CaCO3 into Calcium Phosphate Mineral after Exposure to Sodium Phosphate in Vitro: Implications for in Vivo Hydroxyapatite Bone Formation (2015)

Studies indicate that mammalian bone formation is initiated at calcium carbonate bioseeds, a process that is driven enzymatically by carbonic anhydrase (CA). We show that amorphous calcium carbonate (ACC) and bicarbonate (HCO3 (-) ) cause induction of expression of the CA in human osteogenic SaOS-2 cells. The mineral deposits formed on the surface of the cells are rich in C, Ca and P. FTIR analysis revealed that ACC, vaterite, and aragonite, after exposure to phosphate, undergo transformation into calcium phosphate. This exchange was not seen for calcite. The changes to ACC, vaterite, and aragonite depended on the concentration of phosphate. The rate of incorporation of phosphate into ACC, vaterite, and aragonite, is significantly accelerated in the presence of a peptide rich in aspartic acid and glutamic acid. We propose that the initial CaCO3 bioseed formation is driven by CA, and that the subsequent conversion to calcium phosphate/calcium hydroxyapatite (exchange of carbonate by phosphate) is a non-enzymatic exchange process.
Protection Afforded Infectious Bronchitis Virus-Vaccinated Sentinel Chickens Raised in a Commercial Environment (1989)

The protective efficacy of three infectious bronchitis virus (IBV) vaccines for sentinel chickens raised with commercial Delmarva broiler chickens was evaluated during winter 1987. Specific-pathogen-free leghorn sentinel chickens were vaccinated with Massachusetts (Mass) alone, Mass and JMK, or Mass and Arkansas (Ark) combination live vaccines, or they remained unvaccinated. Four weeks post-vaccination, sentinels were placed on broiler farms at weekly intervals for 3 weeks corresponding to weeks 4, 5, and 6 of the broiler growing cycle. Vaccine efficacy was evaluated based on IBV reisolation attempts from tracheal swabbings following a 1-week field exposure period. Sentinel chickens vaccinated with Mass and Ark combination vaccine were best protected against IBV field challenge. Only four IBV isolations were made out of a 3-week total of 36 attempts, for an 11% isolation rate. IBV vaccines containing either Mass alone or Mass and JMK offered much lower levels of protection.
The Angiotensin-Converting Enzyme 2/Angiogenesis-(1–7)/Mas Axis Confers Cardiopulmonary Protection against Lung Fibrosis and Pulmonary Hypertension (2010)

Our observations demonstrate a cardiopulmonary protective role for the ACE2/Ang-(1-7)/Mas axis in the treatment of lung disorders.
The Effect of Preapplication of Corticosteroids on Skin Irritation and Performance of the GlucoWatch G2® Biographer (2004)

Skin irritation due to iontophoresis may limit the frequency of use of devices for drug delivery or transdermal extraction of analytes of clinical interest. This study examined whether preapplication of corticosteroid preparations could reduce skin irritation from iontophoresis used by the GlucoWatch G2 Biographer (Cygnus, Inc., Redwood City, CA) in monitoring interstitial glucose levels frequently and automatically. Numerous corticosteroid preparations were screened to identify formulations that did not interfere with adhesion of the Biographer to the skin or glucose sensing. Kenalog (Westwood-Squibb Pharmaceuticals, Inc., Buffalo, NY) (triamcinolone acetonide) and Cortizone-10 Quick Shot (Pfizer, Inc., New York, NY) (hydrocortisone) sprays were selected and, in a double-masked, randomized, controlled trial, were applied to the forearms of 66 subjects with diabetes and allowed to dry. Biographers were applied and worn for 15 h, and home blood glucose measurements were taken every 30 min to assess accuracy. Irritation was assessed periodically by trained observers and study subjects. Skin irritation was reduced by both corticosteroid sprays, with the fraction of subjects who experienced moderate irritation reduced by 57% and 43% for the Kenalog and Cortizone-10 Quick Shot sprays, respectively. The treatment effect persisted at the 1-week assessment. Preapplication of these preparations did not affect the clinical utility of interstitial glucose readings. Preapplication of Kenalog or Cortizone-10 Quick Shot sprays significantly reduced skin irritation due to iontophoresis, and did not interfere with glucose measurements. This approach may enable the minority of users who experience moderate to severe skin irritation to use the Biographer more frequently for diabetes management.
Covalent Micropatterning of Poly(dimethylsiloxane) by Photografting through a Mask (2005)

A new photografting method to micropattern a covalent surface modification on poly(dimethylsiloxane) (PDMS) provides advantages in simplicity and efficiency. To accomplish the entire process on the benchtop, the PDMS was initially treated with benzophenone dissolved in a water/acetone mixture. This process permitted limited diffusion of the photoinitiator into the PDMS surface. Polymerization of acrylic acid was initiated by exposure of the benzophenone-implanted PDMS to UV radiation through a photomask with a thin aqueous layer of acrylic acid sandwiched between the PDMS and photomask. This procedure resulted in patterned poly(acrylic acid) (PAA) on the PDMS surface. In the modified regions, PAA and PDMS formed an interpenetrating polymer network extending 50 microm into the PDMS with an X-Y spatial resolution of 5 microm. The carboxyl groups of the PAA graft could be derivatized to covalently bond other molecules to the patterned PAA. Two bioanalytical applications of this micropatterned surface were demonstrated: (1) a guide for cell attachment and growth and (2) a substrate for immunoassays. 3T3 cells were shown to selectively localize to modified surface regions where they could be cultured for up to 7 days. Additionally, the micropatterned surface was used to immobilize either protein A or antibody for heterogeneous immunoassays.
Computer assisted design and synthesis of novel aldose reductase inhibitors (1989)

The design and synthesis of phenalene 26 (AY-31,358), an unsubstituted analogue of a tolrestat/ICI-105,552 computer-generated hybrid (7), are reported. Compound 7 was designed by the superimposition of the putative low-energy conformers of tolrestat (1) and ICI-105,552 (6). The more rigid aldose reductase inhibitor sorbinil (2) was used as a template to help discern a common pharmacophore in the three inhibitors. Compound 26 was synthesized as a model and was evaluated as an inhibitor of bovine lens aldose reductase. It was found to exhibit good in vitro activity as well as some in vivo activity in the nerve. It was expected that introduction of the trifluoromethyl and methoxy substituents would enhance the biological activity of model compound 26. As a result of a positive Ames test with 26, however, work has now been directed toward modifying the template in a way so as to eliminate the mutagenicity with retention of biological activity.
Cloning and Characterization of a Nonhemolytic Phospholipase C Gene from Burkholderia pseudomallei (1999)

We cloned and characterized a phosphatidylcholine-hydrolyzing phospholipase C (PC-PLC) gene from Burkholderia pseudomallei. DNA sequence analysis of the gene indicated an open reading frame coding for 700 amino acids with a 34-amino-acid signal peptide. When cleaved, this yields a secreted 73-kDa mature protein. The deduced amino acid sequence exhibited 48% similarity to that of a nonhemolytic PLC from Pseudomonas aeruginosa. The expressed PC-PLC was heat stable, nonhemolytic for sheep erythrocytes, and active between pH 2 and 8. Western blot analysis with sera from melioidosis patients indicated that they produced immunoglobulin M antibodies against this PC-PLC protein.
Monoclonal antibodies to human plasma low-density lipoproteins. I. Enhanced binding of 125I-labeled low-density lipoproteins by combined use of two monoclonal antibodies. (1983)

Four monoclonal antibodies (IgG2b) to human plasma low-density lipoproteins (LDL) have been characterized. The binding affinities of each monoclonal antibody to 125I-labeled LDL were moderately high, ranging from 10(8) to 10(10) L/mol at 4 degrees C, but were reduced by at least 50-70% at 37 degrees C. The maximum binding of each monoclonal antibody was unique, ranging from 20 to 95% of total 125I-labeled LDL, suggesting that LDL particles were immunochemically heterogeneous. One antibody, LP-34, had both high and low binding affinities to LDL. Another, LP-47, exhibited high affinity for isolated LDL, yet reacted poorly with native LDL in plasma, indicating that the conformation of isolated LDL differs from that of native LDL in plasma. Unlike polyclonal serum antibodies, a mixture of four monoclonal antibodies failed to precipitate LDL, but did show a drastic increase in binding to LDL. We found that only two of our monoclonal antibodies were necessary for such synergistic enhancement. We propose that one of the monoclonal antibodies may serve as a catalytic reagent, and discuss the clinical significance of this finding.
Carboxylic Acid (Bio)Isosteres in Drug Design (2013)

The carboxylic acid functional group can be an important constituent of a pharmacophore, however, the presence of this moiety can also be responsible for significant drawbacks, including metabolic instability, toxicity, as well as limited passive diffusion across biological membranes. To avoid some of these shortcomings while retaining the desired attributes of the carboxylic acid moiety, medicinal chemists often investigate the use of carboxylic acid (bio)isosteres. The same type of strategy can also be effective for a variety other purposes, for example, to increase the selectivity of a biologically active compound or to create new intellectual property. Several carboxylic acid isosteres have been reported, however, the outcome of any isosteric replacement cannot be readily predicted as this strategy is generally found to be dependent upon the particular context (i.e., the characteristic properties of the drug and the drug-target). As a result, screening of a panel of isosteres is typically required. In this context, the discovery and development of novel carboxylic acid surrogates that could complement the existing palette of isosteres remains an important area of research. The goal of this Minireview is to provide an overview of the most commonly employed carboxylic acid (bio)isosteres and to present representative examples demonstrating the use and utility of each isostere in drug design.
An FFT-based technique for translation, rotation, and scale-invariant image registration (1996)

This correspondence discusses an extension of the well-known phase correlation technique to cover translation, rotation, and scaling. Fourier scaling properties and Fourier rotational properties are used to find scale and rotational movement. The phase correlation technique determines the translational movement. This method shows excellent robustness against random noise.
Hydrogen bonding interaction of diphenylbarbituric acid and 9-ethyladenine. Crystal structure of a 1:1 complex (2000)

There are several different types of adenosine receptors found in the brain and molecules capable of interacting with the adenine ring system may have an effect on brain activity. Phenobarbital and diphenylhydantoin, two commonly used antiepileptic drugs have been shown to form hydrogen bonded complexes with adenine derivatives. Although 5,5-diphenylbarbituric acid has anticonvulsant properties equivalent to phenobarbital, neither its structure nor possible interactions with adenine have been investigated. 5,5-Diphenylbarbituric acid and 9-ethyladenine were, therefore, cocrystallized and the three-dimensional 1:1 hydrogen bonded complex was determined by X-ray diffraction. The crystals are monoclinic, C2/c, a = 28.457(9), b = 10.633(3), c = 13.995(4) Å, β = 100.20(2)°, Z = 8, R = 0.067 for 1680 reflections with I &gt; 3σ(I). The molecules propagate along the b crystallographic axis in an alternating fashion in which adjacent adenine and barbiturate molecules interact through a pair of hydrogen bonds. Two-fold symmetry related barbiturate carbonyl groups in neighboring planes of hydrogen bonded ribbons are involved in dipoledipole attractive interactions. This hydrogen bonding pattern is compared to patterns found in other barbiturateadenine complexes.Key words: hydrogen bonding, crystal structure, barbiturates, adenine, anticonvulsants.
Transcription termination and polyadenylation in retroviruses (1993)

The provirus structure of retroviruses is bracketed by long terminal repeats (LTRs). The two LTRs (5' and 3') are identical in nucleotide sequence and organization. They contain signals for transcription initiation as well as termination and cleavage polyadenylation. As in eukaryotic pre-mRNAs, the two common signals, the polyadenylation signal, AAUAAA, or a variant AGUAAA, and the G+U-rich sequence are present in all retroviruses. However, the AAUAAA sequence is present in the U3 region in some retroviruses and in the R region in other retroviruses. As in animal cell RNAs, both AAUAAA and G+U-rich sequences apparently contribute to the 3'-end processing of retroviral RNAs. In addition, at least in a few cases examined, the sequences in the U3 region determine the efficiency of 3'-end processing. In retroviruses in which the AAUAAA is localized in the R region, the poly(A) signal in the 3' LTR but not the 5' LTR must be selectively used for the production of genomic RNA. It appears that the short distance between the 5' cap site and polyadenylation signal in the 5' LTR precludes premature termination and polyadenylation. Since 5' and 3' LTRs are identical in sequence and structural organization yet function differently, it is speculated that flanking cellular DNA sequences, chromatin structure, and binding of transcription factors may be involved in the functional divergence of 5' and 3' LTRs of retroviruses.
Induction of T-cell Immunity Overcomes Complete Resistance to PD-1 and CTLA-4 Blockade and Improves Survival in Pancreatic Carcinoma (2015)

Disabling the function of immune checkpoint molecules can unlock T-cell immunity against cancer, yet despite remarkable clinical success with monoclonal antibodies (mAb) that block PD-1 or CTLA-4, resistance remains common and essentially unexplained. To date, pancreatic carcinoma is fully refractory to these antibodies. Here, using a genetically engineered mouse model of pancreatic ductal adenocarcinoma in which spontaneous immunity is minimal, we found that PD-L1 is prominent in the tumor microenvironment, a phenotype confirmed in patients; however, tumor PD-L1 was found to be independent of IFNγ in this model. Tumor T cells expressed PD-1 as prominently as T cells from chronically infected mice, but treatment with αPD-1 mAbs, with or without αCTLA-4 mAbs, failed in well-established tumors, recapitulating clinical results. Agonist αCD40 mAbs with chemotherapy induced T-cell immunity and reversed the complete resistance of pancreatic tumors to αPD-1 and αCTLA-4. The combination of αCD40/chemotherapy plus αPD-1 and/or αCTLA-4 induced regression of subcutaneous tumors, improved overall survival, and conferred curative protection from multiple tumor rechallenges, consistent with immune memory not otherwise achievable. Combinatorial treatment nearly doubled survival of mice with spontaneous pancreatic cancers, although no cures were observed. Our findings suggest that in pancreatic carcinoma, a nonimmunogenic tumor, baseline refractoriness to checkpoint inhibitors can be rescued by the priming of a T-cell response with αCD40/chemotherapy.
Diffusion of photogenerated acid in chemical amplification positive deep UV resists. (1991)

A new simple method was developed to estimate the diffusion range of photogenerated acid in chemical amplification resist systems. The acid mobility was investigated for various process conditions. It was found that prebake and post-exposure-bake conditions have strong influence on the mobility of acid. The diffusion range of acid is much larger than values estimated from the catalytic volume. No acid diffusion could be detected at room temperature over a period of 2 days. Acid from an opium salt acid generator showed a stronger diffusion than acid from a methanesulfonic acid ester.
Cellobiose Uptake in the Hyperthermophilic Archaeon Pyrococcus furiosus Is Mediated by an Inducible, High-Affinity ABC Transporter (2001)

The hyperthermophilic archaeon Pyrococcus furiosus can utilize different beta-glucosides, like cellobiose and laminarin. Cellobiose uptake occurs with high affinity (K(m) = 175 nM) and involves an inducible binding protein-dependent transport system. The cellobiose binding protein (CbtA) was purified from P. furiosus membranes to homogeneity as a 70-kDa glycoprotein. CbtA not only binds cellobiose but also cellotriose, cellotetraose, cellopentaose, laminaribiose, laminaritriose, and sophorose. The cbtA gene was cloned and functionally expressed in Escherichia coli. cbtA belongs to a gene cluster that encodes a transporter that belongs to the Opp family of ABC transporters.