gebhart/patrepeval huggingface dataset:
FUZZY LOGIC MODEL FOR PREDICTING PEANUT MATURITY (2000)

Peanut quality and yield are impacted by harvest timing. The most commonly used tool for determiningharvest timing is the hull-scrape chart giving association of kernel maturity to color of mesocarp. The hull-scrapetechnique is tedious, time-consuming, and labor-intensive. Wider use of maturity evaluations would be greatly facilitatedby a quicker and easier test. While testing for maturity, the NMR signals from peanuts and days after planting exhibit anonlinear relationship with the maturity class of kernels. Therefore, linear classification techniques such as lineardiscriminant analysis (LDA) may not achieve good classification results. This article describes the development of afuzzy model to predict peanut maturity based on NMR-signal (FIDPK) and days after planting (DAP). Compared to thehull-scrape method, the fuzzy model predictions were 45%, 63%, and 73% accurate when maturity was classified in6 classes, 5 classes and 3 classes, respectively. The respective accuracies from LDA, using the same data, were 42%, 56%and 70%. Data from 346 kernels were used for performance evaluation of both the fuzzy and LDA models. The fuzzymodel improved maturity prediction compared to LDA. These results are encouraging, however, fuzzy model should befurther evaluated with new data.
A phase 2 study of liposomal irinotecan with 5-fluorouracil and leucovorin in squamous cell carcinoma of head and neck or esophagus after prior platinum-based chemotherapy or chemoradiotherapy. (2021)

6025 Background: Liposomal irinotecan (nal-IRI) + 5-FU/LV has been approved and used in treating patients with metastatic pancreatic cancer after gemcitabine-based therapy through the NAPOLI-1 study result. This phase 2 trial evaluated the activity of NAPOLI-1 regimen in patients with squamous cell carcinoma (SCC) of head and neck (H&amp;N) or esophagus that progressed on or recur after platinum-based chemotherapy or concurrent chemoradiotherapy. Methods: Patients with histologically confirmed SCC of H&amp;N or esophagus whose disease progressed while on or progressed/recurred within 6 months after platinum-based chemotherapy or chemoradiotherapy, and unsuitable for further surgical or radiation intervention were eligible. Prior anti-EGFR or anti-PD1/anti-PDL1 treatment was allowed. The regimen consisted of nal-IRI 70 mg/m 2 (irinotecan free base) followed by LV 400 mg/m 2 and 5-FU 2400 mg/m 2 , every 2 weeks. A Simon’s 2-stage design was used with planned 30 evaluable patients in the first stage and 52 evaluable patients in total. The primary endpoint is objective tumor response. Results: From December 2018 to April 2020, 59 subjects were enrolled, including 16 with esophagus cancer and 43 with H&amp;N cancer. Thirty-seven (63%) patients had metastatic disease at enrollment. The mean of treatment cycles were 5 (range, 1-21). Among the total 59 enrolled subjects, 53 subjects (14 esophagus cancer, 39 H&amp;N cancer) were evaluable for objective tumor response. The disease control rate in esophagus cancer was 50% (7 SD, intent-to-treat (ITT) population 43.8%). For H&amp;N patients, 1 CR, 4 PR, and 23 SD resulted in the response rate 12.8% (11.6% in ITT population) and disease control rate 72% (65% in ITT population). The median progression free survival (N = 59) was 2.5 months (esophagus/H&amp;N: 1.5/2.7 months) and the median overall survival was 5.9 months (esophagus/H&amp;N: 4.2/7.3 months). Seventy-eight percent of patients had ≥grade 3 treatment-related adverse events. The most frequent ≥grade 3 toxicities were decreased lymphocyte count (50.8%), decreased neutrophil count (42.4%), and decreased white blood count (33.9%). Only 3 patients (5%) had grade 3 diarrhea during the treatment period. Conclusions: This study showed the modest efficacy and manageable toxicity profile of nal-IRI+5-FU/LV in platinum-refractory locally advanced or metastatic H&amp;N or esophagus cancer patients. Clinical benefits including complete tumor response were noted in H&amp;N patients. The role of this regimen in selective patients and the efficacy of combination with immunotherapeutic agents warrant further explorations. Clinical trial information: NCT03712397.
Inhibition of Cyclooxygenase 2 Synthesis Suppresses Herpes simplex Virus Type 1 Reactivation (2005)

Recurrent herpes virus infection, in which the virus reactivates from the nervous system and causes painful lesions in peripheral tissues, is a significant clinical problem. Our recent studies showing that the amount of cyclooxygenase 2 (COX-2) in the trigeminal ganglia of heat-stressed untreated mice is higher than the amount in heat-stressed mice treated with the COX-2 inhibitor, celecoxib, have indicated that the prostaglandin synthesis pathway--and in particular COX-2--may be an intermediate in the pathway to herpes viral reactivation. To further study this process, we infected the corneas of mice using topical application to a lightly scratched epithelium and waited 30 days for Herpes simplex virus type 1 (HSV-1) latency to be established in the trigeminal ganglia. Prior to the induction of viral reactivation, the mice were treated orally with celecoxib. Treated and untreated mice were induced to undergo reactivation by immersion in 43 degrees C water for 10 min. The shedding of virus at the ocular surface was determined by culturing ocular swabs with indicator cells. The presence of infectious virus in the trigeminal ganglion was evaluated by incubating ganglion homogenates with indicator cells and observing for cytopathic effect. Celecoxib treatment significantly suppressed viral reactivation when given prophylactically by the gastrointestinal route. The numbers of corneas and ganglia containing infectious virus were significantly lower in the celecoxib-treated animals, compared to the placebo-treated mice. These experiments demonstrate that a selective COX-2 inhibitor can suppress hyperthermic stress-induced herpes viral reactivation in the nervous system. It may be possible to use COX-2 inhibitors to prevent viral reactivation in high-risk patients by drug prophylaxis.
Selective cancer cell killing by α-tocopheryl succinate (2001)

We report that alpha-tocopheryl succinate, a vitamin E analogue with pro-apoptotic properties, selectively kills cells with a malignant or transformed phenotype, i.e. multiple haematopoietic and carcinoma cell lines, while being non-toxic to normal, i.e. primary and non-transformed cells. These findings strongly suggest a potential of this micronutrient in the therapy and/or prevention of cancer without significant side-effects.
Oblivious Decision Trees and Abstract Cases (1994)

In this paper, we address the problem of case-based learning in the presence of irrelevant features. We review previous work on attribute selection and present a new algorithm, Oblivion, that carries out greedy pruning of oblivious decision trees, which effectively store a set of abstract cases in memory. We hypothesize that this approach will efficiently identify relevant features even when they interact, as in parity concepts. We report experimental results on artificial domains that support this hypothesis, and experiments with natural domains that show improvement in some cases but not others. In closing, we discuss the implications of our experiments, consider additional work on irrelevant features, and outline some directions for future research.
Long-lasting memory T cell responses following self-limited acute hepatitis B. (1996)

The molecular and cellular basis of long-term T cell memory against viral antigens is still largely undefined. To characterize anti-viral protection by memory T cells against non-cytopathic viruses able to cause acute self-limited and chronic infections, such as the hepatitis B virus (HBV), we studied HLA class II restricted responses against HBV structural antigens in 17 patients with acute hepatitis B, during the acute stage of infection and 2.2 to 13 yr after clinical resolution of disease. Results indicate that: (a) significant T cell proliferative responses to HBV nucleocapsid antigens were detectable in all patients during the acute phase of infection and in 14/17 also 2-13 yr after clinical resolution of disease; b) long-lasting T cell responses were sustained by CD45RO+T cells, predominantly expressing the phenotype of recently activated cells; c) limiting dilution analysis showed that in some patients the frequency of HBV-specific T cells was comparable to that observed in the acute stage of infection and, usually, higher than in patients with chronic HBV infection; d) the same amino acid sequences were recognized by T cells in the acute and recovery phases of infection; and e) HBV-DNA was detectable by nested-PCR in approximately half of the subjects. to conclusion, our results show that vigorous anti-viral T cell responses are detectable in vitro several years after clinical recovery from acute hepatitis B. Detection of minute amounts of virus in some recovered subjects suggests that long-term maintenance of an active anti-viral T cell response could be important not only for protection against reinfection but also for keeping the persisting virus under tight control.
Prevention of Intracerebral Haemorrhage (2007)

Nontraumatic intracerebral haemorrhages arise from a wide range of causes falling into two broad groups: discreet vascular "ictohaemorrhagic" lesions such as aneurysms, arteriovenous malformations, cavernomas, tumours, and dural fistulae; and more generalised amyloid or hypertension related conditions. It is now possible using family history, associated risk factors and gradient echo MRI to predict cases at high risk of hypertensive or amyloid related haemorrhage. There is considerable potential for prevention of hypertensive haemorrhages by treatment of high risk cases with antihypertensive medication. As yet no effective preventative treatment for amyloid angiopathy related ICH has emerged although a variety of drugs are under investigation. Prevention of haemorrhage from ictohaemorrhagic lesions revolves around removal or obliteration of the lesion. Although there is a wide range of such lesions available treatments come down to three modalities. These are surgical excision, stereotactic radiosurgery and endovascular embolisation.
IUPAC-IUB Commission on Biochemical Nomenclature. Rules for naming synthetic modifications of natural peptides. Tentative rules (1967)

During the last few years, chemists have made many compounds that are variants of naturally occurring peptides (or proteins) having trivial names. Therefore, the need has arisen for 'semitrivial' names to designate these variants without the necessity of designating every residue in the chain.
Ultralow-Dielectric-Constant Films Prepared from Hollow Polyimide Nanoparticles Possessing Controllable Core Sizes (2008)

Polyimide (PI) is a candidate material that is showing promise for use in a wide range of applications in several advanced technologies. In this study, we employed the reprecipitation method and subsequent imidization to prepare unique hollow PI nanoparticles (NPs) by blending a suitable polymer porogen with the PI precursor in the form of individual NPs. The hollow structures were induced through phase separation between the PI and the porogen, a process that was influenced by the compatibility between the two polymers. We then assembled multilayered films by depositing the hollow PI NPs electrophoretically onto a substrate. After spin-coating a solution of the PI precursor and then subjecting the system to thermal treatment, the individual PI NPs were bound to their adjacent neighbors, thereby improving the film strength to some extent. We obtained dense, uniformly packed films having controlled thicknesses in the range from 500 nm to 10 μm. This strategy provided films in which air voids existed between and within the composite PI NPs; as a result, the dielectric constant reached as low as 1.9.
Self-assembly of a novel macrotricyclic Pd(ii) metallocage encapsulating a nitrate ion (2001)

Complexation of the ligand 1 with Pd(NO3)2 leads to the self-assembly of a very stable M2L4 type macrotricyclic cage that encapsulates a nitrate ion inside its cavity.
WebSeer: An Image Search Engine for the World Wide Web (1996)

Because of the size of the World Wide Web and its inherent lack of structure, finding what one is looking for can be a challenge. PC-Meter&amp;apos;s March, 1996, survey found that three of the five most visited Web sites were search engines. However, while Web pages typically contain both text and images, all the currently available search engines only index text. This paper describes WebSeer, a system for locating images on the Web. WebSeer uses image content in addition to associated text to index images, presenting the user with a selection that potentially fits her needs. 1 This work was supported in part by ONR contract N00014-93-1-0332 and NSF Grant No. IRI-9210763A01. 2 Introduction The explosive growth of the World Wide Web has proven to be a double-edged sword. While an immense amount of material is now easily accessible on the Web, locating specific information remains a difficult task. An inexperienced user may find it next to impossible to find the information she wants; even a...
The Signal Peptide of the Junin Arenavirus Envelope Glycoprotein Is Myristoylated and Forms an Essential Subunit of the Mature G1-G2 Complex (2004)

Arenaviruses comprise a diverse family of rodent-borne viruses that are responsible for recurring and emerging outbreaks of viral hemorrhagic fevers worldwide. The Junín virus, a member of the New World arenaviruses, is endemic to the pampas grasslands of Argentina and is the etiologic agent of Argentine hemorrhagic fever. In this study, we have analyzed the assembly and function of the Junín virus envelope glycoproteins. The mature envelope glycoprotein complex is proteolytically processed from the GP-C precursor polypeptide and consists of three noncovalently associated subunits, G1, G2, and a stable 58-amino-acid signal peptide. This tripartite organization is found both on virions of the attenuated Candid 1 strain and in cells expressing the pathogenic MC2 strain GP-C gene. Replacement of the Junín virus GP-C signal peptide with that of human CD4 has little effect on glycoprotein assembly while abolishing the ability of the G1-G2 complex to mediate pH-dependent cell-cell fusion. In addition, we demonstrate that the Junín virus GP-C signal peptide subunit is myristoylated at its N-terminal glycine. Alanine substitution for the modified glycine residue in the GP-C signal peptide does not affect formation of the tripartite envelope glycoprotein complex but markedly reduces its membrane fusion activity. In contrast to the classical view that signal peptides act primarily in targeting nascent polypeptides to the endoplasmic reticulum, we suggest that the signal peptide of the arenavirus GP-C may serve additional functions in envelope glycoprotein structure and trafficking.
Control of Calcite Crystal Morphology by a Peptide Designed To Bind to a Specific Surface (1997)

Many organisms contain proteins which regulate the size and shape of inorganic crystals in their skeletal elements, most likely through specific protein−crystal surface interactions. As a model for better understanding such control of crystal morphology, an α-helical peptide (CBP1) was synthesized having an array of aspartyl residues designed to bind to the {11̄0} prism faces of calcite. When added to a saturated solution of calcium bicarbonate containing rhombohedral calcite seed crystals, CBP1 had a remarkable effect on subsequent calcite growth, depending on growth conditions. At 3 °C, where CBP1 is 89% helical, the crystals assumed a prismatic habit, with growth continuing along the c-axis, but inhibited parallel to the c-axis and prism faces; at 25 °C, where CBP1 is largely unstructured, studded crystals formed, resulting from epitaxial growth off each of the six rhombohedral surfaces. Other acidic peptides also caused similar epitaxial growth. These results suggest that the helical form of the peptide recognizes specific crystal surface characteristics, whereas the unfolded form acts nonspecifically as a polyanion. When the peptide was removed from the growth medium containing either type of crystal, regrowth of {104} rhombohedral surfaces ensued at the expense of the nonrhombohedral surfaces. These results represent the first example of conformation-dependent control of calcite crystal growth by a peptide of defined secondary structure.
Antifertility effects of porcine zona pellucida-3 immunization using permissible adjuvants in female bonnet monkeys ( Macaca radiata ): reversibility, effect on follicular development and hormonal profiles (1994)

Female bonnet monkeys Macaca radiata (n = 8, four per group) were immunized with purified 55 kDa glycoprotein from porcine zona pellucida (ZP3) and ZP3 conjugated to the beta subunit of human chorionic gonadotrophin (beta hCG) using adjuvants permissible for human use (alum, muramyl dipeptide and sodium phthalyl derivative of lipopolysaccharide). The animals were monitored for anti-ZP3 antibody titres, biweekly progesterone concentrations, menstrual cyclicity and status of fertility. All the animals generated a good anti-ZP3 antibody response, continued to have ovulatory cycles, remained infertile in the presence of high anti-ZP3 antibody titres and showed no disturbance in cyclicity (except summer amenorrhoea). Examinations by laparoscope showed normal ovaries with developing follicles or corpora lutea on the surface. Fifty per cent of the animals conceived after a decline in antibody titres. Ovaries of animals that failed to regain fertility were examined for changes in morphology at times when anti-ZP3 antibody titres in the circulation were low and following a booster when titres were high. None of the ovaries showed any sign of inflammation or lymphocytic infiltration. Follicles at different stages of development were seen in all of the ovaries. No significant reduction in the number of follicles, except in one monkey (MRA 178), was observed. There was no increase in the numbers of atretic or degenerating follicles. The results showed that ZP3 immunization with permissible adjuvants could be used for immunocontraception without obvious ovarian changes.
Synthesis of (+)-trans-Whisky Lactone, (+)-trans-Cognac Lactone and (+)-Eldanolide (1990)

A new and useful synthesis of I+)-trans-whisky lactone ( 3 1 , it)-trans-cognac lactone ( 4 ) and I+)-eldanolide ( 5 ) starting from levoglucosenone (1) is described.1 2 .P h y s i c a l d a t a f o r o u r s y n t h e t i c 5 a r e as f a l l o w s ; b p 1 1 5 -1 1 l 0 C / 2 1 torr; n ~2 3 1 .4 6 0 6 ; i r ( f i l m ) v c m -I 2 9 7 2 ,2 9 2 0 ,1 7 8 3 ,1 2 1 4 ,1 1 9 5 ; IH-nrnr (CDC13, 3 0 0 MHz): 6 1 . 1 4 13H, d , J = 6 .5 Hz), 1 .6 4 (3M, s ) , 1 .7 3 (3H, s ) , 2 . 1 0 -2 .5 0 (4H, r n ) , 2 .6 8 ( l H , d d , J = 7 .5 a n d 1 6 .6 H z ) , 4 .0 6 (18, d d , J = 6 .5 a n d 1 2 . 2 H z ) , 5 . 1 0 -5 . 2 2 ( I H , 1 3 .O p t i c a l l y a c t i v e e l d a n o l i d e 15) h a s been p r e p a r e d ; a) J .P .V i g n e r o n , R .M e r i c , M .L a r c h e v e q u e .A .D e b a l , G .K u n e s c h , P .Z a g a t t i , a n d M .G a l l o i s , T e t r a h e d r o n W . , 1 9 8 2 , 2 3 , 5 0 5 1 .b ) T .Uernatsu, T .Urnernura, a n d K .Mori, U .U. m ., 1 9 8 3 , 4 7 , 5 9 7 .U ., 1 9 8 3 , 1 2 4 5 .d l K .S u r u k i , T .Ohkuma, a n d G. T s u c h i h a s h i , T e t r a h e d r o n m ., i 9 8 5 , 2 6 , 8 6 1 .el R .M. O r t u n o , R. Merce, a n d J .F o n t , T e t r a h e d r o n , 1 9 8 7 , 4 3 , 4 4 9 7 .
Multiple Residues in the Second Extracellular Loop Are Critical for M3 Muscarinic Acetylcholine Receptor Activation (2007)

Recent studies suggest that the second extracellular loop (o2 loop) of bovine rhodopsin and other class I G protein-coupled receptors (GPCRs) targeted by biogenic amine ligands folds deeply into the transmembrane receptor core where the binding of cis-retinal and biogenic amine ligands is known to occur. In the past, the potential role of the o2 loop in agonist-dependent activation of biogenic amine GPCRs has not been studied systematically. To address this issue, we used the M(3) muscarinic acetylcholine receptor (M3R), a prototypic class I GPCR, as a model system. Specifically, we subjected the o2 loop of the M3R to random mutagenesis and subsequently applied a novel yeast genetic screen to identity single amino acid substitutions that interfered with M3R function. This screen led to the recovery of about 20 mutant M3Rs containing single amino acid changes in the o2 loop that were inactive in yeast. In contrast, application of the same strategy to the extracellular N-terminal domain of the M3R did not yield any single point mutations that disrupted M3R function. Pharmacological characterization of many of the recovered mutant M3Rs in mammalian cells, complemented by site-directed mutagenesis studies, indicated that the presence of several o2 loop residues is important for efficient agonist-induced M3R activation. Besides the highly conserved Cys(220) residue, Gln(207), Gly(211), Arg(213), Gly(218), Ile(222), Phe(224), Leu(225), and Pro(228) were found to be of particular functional importance. In general, mutational modification of these residues had little effect on agonist binding affinities. Our findings are therefore consistent with a model in which multiple o2 loop residues are involved in stabilizing the active state of the M3R. Given the high degree of structural homology found among all biogenic amine GPCRs, our findings should be of considerable general relevance.
The 12th–14th type III repeats of fibronectin function as a highly promiscuous growth factor-binding domain (2010)

It has recently been shown that some growth factors (GFs) have strong interactions with nonproteoglycan extracellular matrix proteins. Relevant here, the 12th-14th type three repeats of fibronectin (FN III12-14) have been shown to bind insulin-like growth factor binding-protein-3, fibroblast growth factor (FGF)-2, and vascular endothelial growth factor (VEGF)-A with high affinity. Since FN III12-14 is known to bind GFs from different families, we hypothesized that this domain could be highly promiscuous in its GF-binding capacity. We used biochemical approaches and surface plasmon resonance to investigate such interactions with recombinant FN III12-14. We found that FN III12-14 binds most of the GFs from the platelet-derived growth factor (PDGF)/VEGF and FGF families and some GFs from the transforming growth factor-β and neurotrophin families, with K(D) values in the nanomolar range, without inhibiting GF activity. Overall, 25 new binding interactions were identified. In a clinically relevant fibrin matrix, a fibrin-binding variant of FN III12-14 was highly effective as a GF delivery system. For instance, in matrices functionalized with FN III12-14, PDGF-BB-induced sprouting of human smooth muscle cell spheroids was greatly enhanced. We show that FN III12-14 is a highly promiscuous ligand for GFs and also holds great potential in clinical healing applications.
Minimal Braid in Applied Symbolic Dynamics (2003)

Based on the minimal braid assumption, three-dimensional periodic flows of dynamical a system are reconstructed in the case of unimodal map, and their topological structures are compared with those of the periodic orbits of the Rössler system in phase space through the numerical experiment. The numerical results justify the validity of the minimal braid assumption which provides a suspension from one-dimensional symbolic dynamics in the Poincaré section to the knots of three-dimensional periodic flows.