bluuebunny/crossref_metadata_2025_split huggingface dataset:
Introduction
Authors: Hemion Geoffrey 
Published: November 2023

Abstract
People have always found knots to be fascinating and frustrating. A ‘knotty problem’ is difficult to solve. If we allow ourselves to become entangled in the intricacies of such a problem, then we will be ‘tied in a knot’. One way out may be to follow the example of Alexander in his conquest of Asia. He simply drew his sword and slashed through the Gordian knot, reducing things to the level of mere destruction! Knots, along with pyramids and pendulums, have formed the basis of obscure speculations in the realms of the occult. Organic chemists claim that their molecules may form knots or links. Mathematical physicists have declared that physical space is of a stringy nature. As far as pure mathematics is concerned, knot theory has been studied seriously for more than a hundred years. Hundreds of papers have been published during that time. Many strange and delightful facts have been uncovered. But surely the main mathematical question concerns the classification of knots. If Alexander had been a philosopher then he would have attempted to determine whether or not the Gordian knot could be unknotted; that is, shown to be equivalent to the trivial knot. Slightly more general is the problem of comparing two arbitrary knots with one another.
Numerical Methods and Scientific Computing
Authors: Kockler Norbert 
Published: November 2023

Abstract
The book covers the whole range of numerical mathematics from linear equations to ordinary differential equations with short sections on the calculus of errors and on partial differential equations. It attempts to give a unified approach of theory, algorithms, applications and use of software. Therefore it contains only a few proofs but many examples and applications. This book is appearing simultaneously with the problem-solving environment PAN. The PAN system contains an enlarged hypertext version of the text, together with all the programs described in the text, help systems, and utility tools. PAN is licensed public domain software. This parallel appearance of paper and electronic versions including additional useful software is unique. There are four appendices, which describe PAN, the programs written for PAN that are used in the text for examples and applications, and the NAG Fortran and NAG Graphics Libraries used by the programs.
Irregular Sampling
Authors: Higgins J R 
Published: November 2023

Abstract
A sampling process employing sample points that are not equidistantly spaced is usually called irregular, or sometimes non-uniform. Irregular sampling arises mathematically by simply asking the question “What is special about equidistantly spaced sample points?”; and then finding, as we shall in this chapter, that the answer is “Within certain limitations, nothing at all”.In practice it is often said that irregular sampling is the norm rather than the exception. For example, sample points are likely to be disturbed by “noise”, meaning any random influences beyond our control. Again, it might he convenient to reconstruct a function from the locations of its zeros, or places where it crosses some datum function. Such points are, of course, intrinsic to the object function.Again, sample points might be required to have a deterministic distribution, and then we ask if all functions of a given class can be reconstructed from their samples at these points. This is the only kind of irregular sampling we shall discuss here. A review of the applied aspects of irregular sampling can be found in Marvasti (1993), and there are many interesting studies on this theme in the Conference Proceedings of the 1995 workshop on sampling theory and applications, Jurmala, Latvia, 1995, published by the Institute of Electronics and Computer Science, Riga, Latvia.
A comprehensive classification of homeobox genes
Authors: Burglin Thomas R 
Published: November 2023

Abstract
The homeodomain was originally described as a highly conserved protein motif of 60 to 63 amino acids, encoded by a short DNA fragment, the horneobox, that was found in Drosophila developmental control genes (McGinnis et al., 1984; Scott and Weiner, 1984). As more and more homeobox-containing genes were isolated it became obvious that for closely related homeodomains the sequence similarity could be extended upstream and/or downstream of the core 60 amino acids (for a previous compilation, see Scott et al., 1989). In contrast, highly divergent homeodomain sequences have been identified for which the sequence similarity is shorter than the orig inally defined 60 amino acids. The definition of the homeodomain used here is based on the canonical 60 amino acid core as it is most often used.
SEC67
Authors: Feldheim D A 
Published: November 2023

Abstract
Sec67p was identified as a 23 kDa protein that co-precipitated in an immune complex with Sec62p when radiolabeled, detergent solubilized membrane proteins were immunoprecipitated with anti-Sec62p antibodies under non-denaturing conditions1. Subsequently it was shown that anti-Sec63p antibodies also co-immunoprecipitate Sec67p2 Sec67p was purified in quantities suitable for microsequencing using large-scale immunoprecipitation.
SEC72
Authors: Green N 
Published: November 2023

Abstract
A mutant allele (sec72-1) was isolated based on its inability to insert into the membrane of the ER a membrane-bound fusion protein consisting of the N-terminal 255 residues of arginine permease and the complete histidinol dehydrogenase sequence encoded by the HIS4C region of H/5412 The histidinol dehydrogenase portion of the fusion protein was poorly translocated across the ER membrane in sec72-1 mutant cells. This mutant was also defective in translocation of the dehydrogenase when it was placed behind only the N-terminal 189 residues of the permease and in the insertion of another membrane-bound fusion protein containing an N-terminal segment of Sec63p fused to invertase, a glycosylated reporter protein.
EUG1
Authors: Ekena K , LaMantia, M , Steven T 
Published: November 2023

Abstract
EUG1 (I;R protein necessary for growth under standard laboratory conditions) was named for its observed mutant phenotype. Overproduction or deletion of the EUG1 gene appears to have no effect on cell viability or function. Yeast cells deleted for EUG1 grow with wild-type rates on rich or minimal media at temperatures from 18°( to 40°( and can grow anaerobically. Sporulation is not affected in homozygous eug1t,, cells, nor is the transport of vacuolar and secreted proteins through the secretory pathway. Finally, eug1 cells do not exhibit any increased sensitivity or requirement for calcium.
SHR3
Authors: Ljungdahl P O , Fink G R 
Published: November 2023

Abstract
Spontaneous yeast mutants resistant to 30 mM histidine were isolated1· Genetic analysis indicates that super high histidine resistant (shr} mutants resulted from recessive mutations in single genes defining nine complementation groups. Mutations in the SHR3 gene confer resistance to high concentrations of histidine by pleiotropically inhibiting the functional expression of the general amino acid permease (GAP1} and at least 10 specific high affinity amino acid permeases.
WBP1
Authors: Aebi M , Heescn S te 
Published: November 2023

Abstract
The Wbp1 protein was purified by virtue of its binding to the lectin wheat germ agglutinin (Wbp1 = heat germ agglutinin _binding Qrotein 1) and the monoclonal antibody RL112. Oligonucleotide probes were designed using N-terminal and internal peptide sequences of the protein and used to screen a plasmid library of yeast genomic DNA.
PMR1
Authors: Antebi A , Fink G R 
Published: November 2023

Abstract
PMR1 encodes a non-essential secretory protein whose absence neither leads to inviability nor impedes secretory transport. In fact, the original mutant (previously called ssc1-1) was isolated as one of two complementation groups having “supersecretor” activity, the ability to secrete yeast/mammalian heterologous proteins which in wild-type strains remain trapped within the ceI11. The acquisition of the gene and the construction by molecular genetic techniques of strains carrying a pmr1 deletion allele confirmed that the original ssc1 phenotype represents pmr1 loss of function2. This ability does not reflect an overall increase in the rate of normal secretory transit, as the half-time of secretion of the endogenous yeast protein, invertase, is approximately the same for mutant and wildtype strains (4 and 5 minutes respectively)3.
SEC14
Authors: Bankaitis V 
Published: November 2023

Abstract
Mutants harboring conditional-lethal mutations were isolated using a Ludox density enrichment method and found to exhibit a terminal phenotype of exaggerating intracellular toroid structures interpreted to represent dysfunctional yeast Golgi9 Indeed, within 15 min of shift to a restrictive temperature, sec14rs mutants display a secretory block and accumulate fully-glycosylated secretory proteins within the ce11.
KtX1
Authors: Cooper A , Bussey H 
Published: November 2023

Abstract
kex1 mutants were originally isolated due to their reduced production of active K1 killer toxin (killer expression). In addition, such mutants, although not sterile for yeast mating, produce a partially processed form of a-factor pheromone with less biological activity than mature a-factor produced by KEX1 strains1 Cellular extracts prepared from kex1 strains lack a membrane-bound carboxypeptidase activity specific for basic residues2 The growth rate of strains containing disruptions of the KEX1 locus are not significantly different from those of the wild-type KEX1 strain1.
SNAP
Authors: Brunner M , Whiteheart S W 
Published: November 2023

Abstract
SNAP proteins purified from bovine brain tissue were digested by proteases3. Amino acid sequence analyses of SNAP peptides were used to design degenerate oligonucleotide primers and SNAP specific probes were then amplified from a bovine brain cDNA library using the polymerase chain reaction. These probes were then used to screen a ).,gt10 library3 and clones encoding a-, 13-, and y-SNAPS were obtained. The cDNA clones contain open reading frames of 885, 894 and 984 nucleotides, encoding proteins with predicted M,s of 33 kDa, 34 kDa and 36 kDa, respectively, for a-, 13-, and y-SNAPS. a- and 13-SNAP are identical to each other and 34% and 33% identical, respectively, to 5.
V1PS18/PEP3
Authors: Robinson K S , Emr S D 
Published: November 2023

Abstract
Haploid yeast strains in which the entire open reading frame of the VPS18 gene has been deleted are viable12. Such vps1B!l cells have only a slight growth defect at lower temperatures but cannot divide at 37°C. The mutant cells mislocalize and secrete (&gt;95%) the precursor form of the soluble vacuolar hydrolase carboxypeptidase Y (CPY) even at lower temperatures (20°C and 30°(). Precursors of other soluble vacuolar hydrolases are also mislocalized.
VPS34
Authors: Stack J H , Herman, P K , Emr S D 
Published: November 2023

Abstract
vps34 mutants exhibit a temperature-sensitive growth defect and are sensitive to osmotic stress. Deletion of the VPS34 gene results in a ts growth defect, indicating that the VPS34 gene is required for vegetative growth only at elevated temperatures1. vps34 mutants exhibit a defect in bud vacuole inheritance as indicated by the fact that no vacuolar structures were observed in the newly emerging bud in 80% of dividing vps34 cells1. Such a vacuole segregation defect is typical of class D vps mutants5 vps34 cells are defective in the proper sorting of a variety of yeast vacuolar proteins, including proteinase A, proteinase B, and carboxypeptidase Y13 &gt;95% of the newly synthesized carboxypeptidase Y is mislocalized and secreted from vps34 cells as a Golgi-modified precursor form.
PEP8
Authors: Bachhawat A K , Jones F W 
Published: November 2023

Abstract
Haploid yeast cells possessing a disruption allele of the PEPB gene are viable and have apparently normal vacuoles as visualized by light microscopy. Pep B mutants are deficient in carboxypeptidase Y (CPY) activity. pepB mutants also secrete the precursor forms of protease A and CPY.
VMA2
Authors: Ho M N , Stevens T H 
Published: November 2023

Abstract
Cells carrying the vma2 null allele are viable, however, these cells are devoid of vacuolar H+-ATPase activity2,5. Vacuoles in vma2 cells are not acidified relative to the cytoplasm as determined by a flow cytometric pH assay2. vma2 strains are defective for growth in medium buffered at a neutral pH, and have a slowed growth rate relative to wild-type cells in acidic medium2·5. vma2 cells grow poorly on medium containing elevated levels of calcium and are unable to grow on non-fermentable medium such as glyceroI2,5,6.
VMAS
Authors: Ho M N , Stevens T H 
Published: November 2023

Abstract
The DNA sequence of the VMA5 gene (GenBank accession # M77143) encodes a hydrophilic protein of 373 amino acids with a predicted molecular mass of 42 kDa. The amino acid sequence of Vma5p shares 37% identity with subunit C of the vacuolar H+-ATPase isolated from bovine kidney microsomes6 The amino acid sequence of Vma5p does not contain an amino-terminal signal sequence or a membrane spanning domain.
VMA11
Authors: Ohya Y , Umemoto, N , Anraku Y 
Published: November 2023

Abstract
Cells carrying the vma11 null allele grow normally in yeast extract-polypeptone-glucose (YPD) medium, however, these cells are devoid of vacuolar H+-ATPase activity1-2 vma11 mutants show a Pet” Cls- (£alcium-2ensitive) phenotype as they cannot utilize nonfermentable carbon sources such as glycerol, lactate and succinate, and cannot grow in YPD-100 mM CaCl2 medium. In YP-glycerol medium, vma11 cells cannot grow (generation time&gt;16 hrs), but most cells are viable even after 16 hr of incubation. More than 80% of the mutant cells die within 2 hr in YPD-100 mMCaCl2 medium.
YPT7
Authors: Wichmann I , Hengst L , Callwitz D , Schmiiller, F , Riezman H 
Published: November 2023

Abstract
Cells carrying a disruption in the YPTl gene exhibit a strong defect in vacuole biogenesis resulting in abnormal fragmentation of that compartment. The maturation of both soluble and membrane-bound vacuolar proteins is extremely delayed in the mutant. Three soluble vacuolar hydrolases, carboxypeptidase Y and proteinases A and B, need up to two hours for complete maturation whereas alkaline phosphatase, a membrane-bound vacuolar enzyme is only partially matured within the same time range. Unlike the vps mutants with fragmented vacuoles, carboxypeptidase Y is not secreted by yptl null mutants1
Cation-dependent mannose 6-phosphatereceptor
Authors: Johnson K F 
Published: November 2023

Abstract
The human, bovine and murine CD-MPR cDNAs (GenBank accession numbers: bovine, #M17025; human, #J02937; mouse, #M63286) all predict a protein of approximately 31 kDa with five potential N-linked glycosylation sites, four of which are utilized1·3. The 67 amino acid cytoplasmic tail is absolutely conserved in the human, bovine, and murine receptors3 There is some amino acid heterogeneity in the extracytoplasmic and transmembrane domains of the CDMPR in these three species. The CD-MPR shows some sequence identity with the cation-independent mannose 6-phosphate receptor (CI-MPR). The entire extracytoplasmic domain of the CD-MPR has 14 to 28% identity with each of the 15 contiguous repeats in the extracytoplasmic domain of the CI-MPR. The two MPRs have potential serine phosphorylation sites and stretches of acidic residues in their cytoplasmic domains.
GTP-binding proteins in plants
Authors: Terryn Nancy , Montagu Marc Van , Inze Dirk 
Published: November 2023

Abstract
Full length cDNAs of small GTP-binding proteins were inserted into PGEM1 under the control of the T7 promotor as described previously (Chavrier et al. 1990; Huber et al. 1993). GTP-binding proteins were then transiently expressed in BHK 21 cells with the T7 RNA polymeraserecombinant vaccinia virus system (Fuerst et al. 1986; Chavrier et al. 1990; Huber et al. 1993, 1994b). Cells were scraped and fractionated 5 hours after infection/transfection and membrane fractions applied to high resolution 2D-gel electrophoresis. After renaturing transfer to nitrocellulose the blots were overlaid with [a-32P] GTP and the GTP-binding profiles visualized by autoradiography.
Dictyastelium discoideum Rab- and Rho-related proteins
Authors: Bush John , Cardelli James 
Published: November 2023

Abstract
We have isolated seven new rho-like cDNAs (Table I; Bush et al. 1993a), five of which encode proteins that are at least 70 percent identical in amino acid sequence to the human Rac1 protein (Drivas eta/. 1990).
Receptors for Interleukin-2 (IL-2)
Authors: Voss S D , Robb R J 
Published: November 2023

Abstract
The a chain (p55, Tac) of the human IL-2 receptor, encoded by a single gene on chromosome 10, p14--15 (Leonard et al. 1985a), is produced as a 272 amino acid (aa) precursor with a 21 aa signal sequence (GenBank accession number K63122) (Leonard et al. 1985b). The mature protein contains a 219 aa extracellular domain, a 19 aa membranespanning region, and an intracellular, carboxy-terminal domain of 13 residues (Fig. 1) (Leonard et al. 1984, 1985b). The difference between the observed molecular weight of 55 000 Oa (SOS-PAGE) and the predicted molecular weight of 28437 Oa is due to N-(Asn 49 and 68) and 0-linked glycosylation and sulphation (Leonard et al. 1985c). The a chain is characterized by an internal repeat of - 65 residues corresponding to exons 2 and 4 of the gene (Leonard et al. 1985b). These segments have 25 per cent homology with each other and limited homology to the Ba fragment of complement factor B. Exon 4 is deleted in a fraction of a chain mRNA (Leonard et al. 1984).
Interleukin-3 (IL-3)
Authors: Schrader J W 
Published: November 2023

Abstract
Multi-lineage colony-stimulating factor, persisting (P)-cellstimulating factor, mast-cell growth factor, burst-promoting activity, Thy-1-stimulating activity, Histamine-producing cell stimulating activity, haemopoietic cell growth factor, multilineage haemopoietic growth factor, CFUsstimulating activity, stem cell-activating factor, haemopoietin-2, synergistic activity, pan specific haemopoietin, and CSF-2a and -2/J.
Receptors for Interleukin-3 (IL-3)
Authors: Ogorochi T , Miyajima A 
Published: November 2023

Abstract
The murine and human IL-3R o. subunit cDNAs (GenBank accession numbers X64534 and M74782) encode a protein of 396 and 378 amino acids including a putative signal peptide of 16 and 18 amino acids, an extracellular domain of 315 and 288 amino acids, a single transmembrane spanning segment of 24 and 20 amino acids, and a cytoplasmic domain of 41 and 52 amino acids, respectively (Fig. 1). The sequence identity between these two a. subunits is 47 per cent at the DNA level and 30 per cent at the amino-acid level. The deduced molecular weights of the murine and human IL-3R a subunits are 41215 Da and 41254 Da, respectively. The observed molecular weights on SOS-PAGE are 60-70 kDa due to glycosylation at several of the predicted five N-glycosylation sites. The extracellular domains contain common features of the class I cytokine receptor family that include four conserved cysteine residues and the WSXWS motif near the transmembrane domain. There is a short strech of amino acid sequence that is conserved among the a subunits ofthe fl-3, IL-5, and GM-CSF receptors (Kitamura eta/. 1991; Hara and Miyajima 1992).
Interleukin-10 (IL-10)
Authors: Nicola N A 
Published: November 2023

Abstract
The nucleotide sequences of interleukin-10 cDNAs cloned from mouse and man (GenBank accession numbers M37897 and M57627, respectively) predict proteins of 178 (human) or 175 (mouse) amino acids each including an amino-acid leader sequence (Moore et al. 1990; Vieira et al. 1991).
Interleukin-12 (IL-12)
Authors: Wolf S F , Nickbarg E 
Published: November 2023

Abstract
cDNAs for human and murine IL-12 subunits have been cloned (Wolf et al. 1991; Gubler et al. 1991; Schoenhaut et al. 1992). The nucleotide sequences of the p40 subunit from man and mouse (GenBank accession numbers M65292, M65272, and M86671) predict polypeptides of 328 and 335 amino acids, respectively. Both include amino terminal sequences, 22 amino acids in length, which are characteristic of hydrophobic signal peptides. At the amino acid level, the p40 subunits are 70 per cent identical and 79 per cent similar.
High Molecular Weight R Cell Growth Factor (Interleukin-14)
Authors: Blumenthal D E , Ford R J , Ambrus J L 
Published: November 2023

Abstract
50-60 kDa forms of IL-14 have been identified in supernatants of normal human Tcells, T-ALLcells, B cell lines, and B cell lymphomas after stimulation with phytohemagglutinin (PHA), and in ascites and pleural fluid from patients with B cell lymphomas (Ambrus and Fauci 1985; Ford et al. 1992). Purified 60 kDa IL-14 from PHA-stimulated Namalva cells or T-ALL cells is glycosylated, and its apparent molecular weight does not change under reducing conditions. lsoelectric focusing reveals that the 60 kDa band can be resolved into two distinct proteinsat pl 6.7 and 7.8, both of which demonstrate B cell growth factor activity (Ambrus and Fauci 1985; Ambrus et al. 1985).
Erythropoietin
Authors: Goldwasser M Gupta ,E 
Published: November 2023

Abstract
Epo was purified from the urine of anaemic patients(Miyake et al. 1977), and the amino acid sequence derived from the purified protein {Lai et al. 1986) led to the cloning of the human epo gene {Lin et al. 1985; Jacobs et al. 1985). Epo is a secreted glycoprotein containing 193 amino acids(human) or 192 amino acids (monkey and mouse) including a hydrophobic leader sequence of 27 amino acids. Approximately 40 per cent of the human recombinant matureprotein is composed of carbohydrate. It has one site (Ser 126) with O-linked glycosylation and three sites {Asn 24, 38,83) with N-linked glycosylation.
The Macrophage Colony-Stimulating Factor (M-CSF) Receptor
Authors: Rohrschneider L R 
Published: November 2023

Abstract
The M-CSF receptor (Fms) is a member of the class Ill family of tyrosine kinase growth factor receptors and is most highly related to the PDGF receptors, c-kit, kdr/flk1 (vascular endothelial cell growth factor receptor), the torso gene product, flt1, flt3/flk2, and flt4. The cDNAs for feline, murine, and human c-fms genes have been cloned (Rohrschneider and Woolford 1991) (GenBank accession numbers J03149, X06368, and X03663, respectively). The predicted amino acid sequences exhibit the general structural features shown in Fig. 1. For the murine receptor, the extracellular, M-CSF-binding domain is composed of 510 amino acids (512 amino acids for human Fms), with a 26-aminoacid transmembrane sequence, and a 440 amino acid cytoplasmic domain (434 amino acids for human Fms). The primary translation product contains a hydrophobic leader sequence of which the N-terminal 19 amino acids are cleaved. N-linked glycosylation is added at up to nine potential sites in murine Fms, 10 sites in feline Fms, and 11 in the human Fms. Seven ofthese sites are common among all three Fms proteins and no O-linked glycosylation is detectable on Fms.
Kit (Stem Cell or Steel Factor) Receptor
Authors: Bernstein A , Motro B 
Published: November 2023

Abstract
The human c-kit receptor gene encodes a 972-amino-acid precursor protein with a predicted 24-amino-acid leader sequence (GenBank accession number X06182) (Yarden et al. 1987). A single predicted transmembrane domain of 23 amino acids divides the protein into two major domains. The amino terminal extracellular 487 amino acids form the ligand-binding domain and are composed of five immunoglobulin-like loops. The predicted molecular weight of the receptor is 109000 but the observed molecular weight on SDS-PAGE gels is 145-160000 due to N-glycosylation at several of the nine potential glycosylation sites. The (terminal intracellular439-amino-acids domain contains the phosphotyrosine kinase domain. The kinase domain is split by a 68-amino-acid kinase insert domain between the ATP binding site and the catalytic phosphotransferase domain.