bluuebunny/crossref_metadata_2025_split huggingface dataset:
EXPERIMENTAL YAWS IN THE MONKEY AND RABBIT
Authors: Nichols Henry J. 
Published: June 2004

1. Rabbits can be infected in the testicle with the spirochetæ of yaws as well as with those of syphilis and the infection can be continued through successive generations in pure culture.
2. The infection shows itself by enlargement of the testicle and the presence of a nodule varying in size from that of a pea to that of an olive. The infection consists in a necrosis of the tubules, an infiltration of round cells and the new formation of an edematous connective tissue.
3. The complement fixation reaction occurs in rabbits infected with the spirochetæ of yaws as well as in those infected with the spirochetæ of syphilis.
4. This lesion makes possible the investigation of the problems of cultivation, of immunity and of treatment.
CHANGES IN THE HEMOSIDERIN CONTENT OF THE RABBIT'S LIVER DURING AUTOLYSIS
Authors: Brown W. H. 
Published: June 2004

1. Hemosiderin may be produced outside of the animal body and is increased in the liver of rabbits, during autolysis, for a period of from twenty-four to forty-eight hours.
2. Post-mortem hemosiderin formation is most marked in parts of livers exposed to air, and hemosiderin is, apparently, an oxidation product of hemoglobin due to enzyme action.
3. Hemosiderin is derived from hemoglobin directly and not from hematin as an intermediate product.
4. The later stages of autolytic changes show that the acid products of proteid autolysis, especially the phosphorus acids, are capable of producing a cleavage of hemosiderin and uniting with the iron to form a new series of products which react microchemically for both phosphorus and iron. In such cleavage, pigments analogous to the bile pigments are formed.
5. The relationship observed between hemosiderin and hematoidin is such as would indicate that hematoidin is the pigment matter of hemosiderin.
6. Further, it seems probable that the vital cycle of hemoglobin metabolism in the liver is largely intranuclear; the hemoglobin is converted into hemosiderin either within the nucleus or cell protoplasm; the iron of the hemosiderin is bound by an acid radicle of the nucleo-proteid, and the hematoidin is excreted as bile pigment.
Rearrangement and expression of T cell receptor genes in cloned murine natural suppressor cell lines
Authors: Hertel-Wulff B , Lindsten T , Schwadron R , Gilbert DM , Davis MM , Strober S 
Published: June 2004

Naturally occurring suppressor cells of the in vitro mixed leukocyte culture reaction and of in vivo graft-vs.-host disease have been identified in the spleens of neonatal mice (1) and of adult mice recovering from total lymphoid irradiation (2), whole-body irradiation (3), and syngeneic marrow transplantation (4), or cyclophosphamide therapy (5). Using both positive and negative selection procedures, the suppressors were reported to be null lymphocytes that did not express mature macrophage surface markers, nor differentiate into mature macrophages in vitro, nor demonstrate natural killer (NK) activity (1). Subsequently, cloned lines of these natural suppressor (NS) cells were derived from either adult mice given total lymphoid irradiation (TLI) (2) or from neonates (6). The cloned NS cell lines expressed a surface phenotype (2, 6) similar to that reported previously for cloned NK cells (Thy-1(+), asialo-GM1(+), Ig(-), Lyt-1(-), Lyt-2(-), Ia(-), MAC-1(-)) (7-9). However, the NS cells did not show NK activity in the standard assay with YAC-1 target cells. The cloned NS lines suppressed the proliferation of responder cells and the generation of cytolytic cells in the mixed leukocyte reaction (MLR), and suppressed lethal graft-vs.-host disease in vivo (10, 11). In view of the unusual function and surface phenotype of the cells, the lineage of these cells remained unclear.
To determine the lineage of the cloned NS cells, we searched for expression and rearrangement of the α and β chain genes of the T cell antigen receptor, as well as that of the γ chain gene. Studies of the phenotypically similar NK cell yielded conflicting results. Thus, cloned lines of murine NK cells were reported to have rearrangements of the β chain genes, and to express mRNA for all three chains (12). In contrast, freshly purified rat or human large granular lymphocytes (LGL) were shown to express only the 1.0 kb mRNA species of the β chain gene (13), indicative of D-J joining (14). Thus, some but not all cells with NK function express the T cell receptor and are members of the T cell lineage. The current report shows that the NS lines express full-length mRNA transcripts for the a and β chain of the T cell receptor, as well as the γ chain gene.
A population of murine hematopoietic progenitors expresses an endogenous retroviral gp70 linked to the Rmcf gene and associated with resistance to erythroleukemia
Authors: Buller RS , Van Zant G , Eldridge PW , Portis JL 
Published: June 2004

Multiple copies of retroviral sequences are stably integrated in the genomes of many higher organisms, and are thus transmitted vertically to offspring via the germline (1). Most of these heritable viral genes are not expressed, and expression, when observed, is commonly limited to envelope (env) genes as demonstrated by the presence of cell surface and serum envelope glycoprotein (gp70) in mice. Studies of the mouse have shown that certain tissues such as the reproductive tract and lymphoid organs are common sites for the expression of endogenous env genes, suggesting that the transcription of at least some endogenous sequences is tissue specific. The transcription of endogenous viral genes is regulated by both cis and trans mechanisms (2-5) and their expression can be temporally linked to differentiation and development (6-8).
The consequences to the host of endogenous retroviral genes are varied. At one extreme, expression of endogenous virus can result in the development of leukemia and death. Another potentially detrimental effect is that of insertional mutagenesis, seen when the integration of retroviral sequences interrupts the functioning of a cellular gene (9, 10). However, it is now clear that expression of endogenous retroviral genes may also have a beneficial effect for the host: namely, mediating resistance to retroviral leukemias as has been demonstrated for the Fv-4 gene in mice (11) and some ea loci in chickens (12). This form of resistance is due to the blockage of cellular viral receptors by the expression of envelope glycoprotein on the cell surface.
The Rmcf locus of the mouse is another resistance gene that may exert its effect by the expression of an endogenous env gene. A summary of our current state of knowledge concerning the Rmcf gene is shown in Table I. The Rmcf gene was originally described when it was observed that fibroblast cell cultures derived from certain strains of mice restricted the replication of recombinant mink cell focus-forming(MCF)1 viruses (13). As detailed in Table I, DBA/2 mice are the prototypic strain exhibiting the Rmcf resistance (Rmcf(r)) phenotype. Cell cultures from other strains, such as C57BL/6 and IRW, are permissive for MCF viral replication and are termed Rmcf sensitive (Rmcf(s)). Previously, we described two allelic forms of an endogenous env gene, whose expression is linked to the Rmcf gene (14). Cell cultures from Rmcf(r) mice express gp70 related to that of MCF viruses, whereas cultures derived from Rmcf(s) mice either express no gp70 (IRW) or express an endogenous xenotropic gp70 (C57BL/6). These two gp70 alleles are detectable by type-specific mAbs.
ON THE EXCRETION OF GLYCURONIC ACID IN PNEUMOCOCCUS INFECTIONS, WITH SPECIAL REFERENCE TO LOBAR PNEUMONIA
Authors: Medigreceanu Florentin 
Published: June 2004

1. It has been found that the amount of glycuronic acid excreted in the urine, estimated by Tollens's furfurol distillation method, is increased during the febrile period of almost all cases of lobar pneumonia in man. Patients weighing from fifty-five to seventy kilograms excrete during the febrile period 0.8 to 1.3 grams of glycuronic acid in twenty-four hours, while the output of a normal individual of the same weight, age, and under similar conditions would not exceed 0.4 to 0.6 of a gram.
2. This increased output is not dependent on outside factors; it is attributable to pathological changes of the organism itself during the disease.
3. Similar observations have been made in postpneumonic empyema and bronchopneumonia.
4. Fasting rabbits, with general pneumococcus infection, have also shown a marked increase in the output of glycuronic acid during the pathological process.
Whether the conjugated substances with the glycuronic acid in the cases studied have the same origin and are qualitatively the same as under normal conditions, or whether we are dealing with different compounds, has not yet been determined.
THE RELATION OF BACTERIOLYSIS TO PROTEOLYSIS
Authors: Jobling James W. , Petersen William 
Published: June 2004

1. There is no demonstrable increase in non-coagulable nitrogen during bacteriolysis.
2. Bacteria treated with immune serum and complement are so altered that they are more readily digested by trypsin.
3. Bacteria treated with complement alone become more resistant to proteolysis.
4. Bacteria treated with an excess of immune serum and complement become more resistant to proteolysis.
STUDIES ON THE CHEMISTRY OF SEROUS EFFUSIONS
Authors: Epstein Albert A. 
Published: June 2004

A comparison of the results obtained in the analysis of the different effusions shows that they vary, (1) according to location, and (2) according to the disease in which they are produced. Thus the subcutaneous effusions are totally different in their composition from the abdominal or pleuritic fluids; and again the abdominal fluid of nephritic origin is different from those of cardiac or other origin.
The cutaneous effusions are characterized by a very low protein content and a small amount of incoagulable nitrogen. Of the protein present in these fluids, the globulin constitutes the greater portion. In the mixed cardionephritic fluids the ratio of globulin to albumin is lower than that in normal blood serum; but when compared with the blood sera of cardionephritic cases there appears to be a certain parallelism. The chloride content of these fluids is considerably above that found in normal blood serum, but is comparable with those of corresponding cases.
The effusions occurring in serous cavities differ from the cutaneous ones by their higher protein content. The highest values are attained in the pleural fluids, in which the protein present is almost the same as that in normal blood serum. The incoagulable nitrogen in these fluids is uniformly low. The chlorides vary in amount according to the nature of the case. In the effusions of inflammatory origin the values are lower than those found in the blood. In the pleural fluids of other than inflammatory origin the chloride content is either the same or higher than that of blood serum. The globulin-albumin ratio in all of these fluids except one (table III, fluid 61) is higher than that of normal blood serum. Otherwise the highest value is presented by a pleural fluid from a case of nephritis (table III, fluid 205) and the lowest by an empyema fluid (table III, fluid 30). The latter case is of especial interest because of the theory, first propounded by Schmidt, that the leucocytes in the purulent fluid are largely responsible for high globulin content.
The abdominal fluids in general are less rich in protein than the pleural effusions. Those of cardiac origin give the highest protein values, but the globulin-albumin ratios are lower than in the pleural fluids or in the blood sera of corresponding cases. Only in two fluids does the globulin reach a percentage of 62 and 52.2. In both these cases the chloride content is also high. The incoagulable nitrogen in all of them is rather low. In one fluid of purely nephritic origin the protein content is low and all of it is globulin. This is suggestive, when compared with the values obtained in the analysis of the blood sera from nephritic cases. The results obtained in the analysis of abdominal fluids from cardionephritic cases approach very closely those obtained in purely cardiac cases.
LIPOIDS AS INHIBITORS OF ANAPHYLACTIC SHOCK
Authors: Jobling James W. , Petersen William 
Published: June 2004

1. The antitryptic titer of the serum can be increased by subcutaneous injections of serum lipoids (antitrypsin) and of the lipoids from egg yolk.
2. Animals so injected show a relative immunity to acute anaphylactic shock (two minimum lethal doses).
3. Extraction of lipoids contained in antigens increases the toxicity of the antigen when injected into a sensitized animal.
4. Sublethal doses of soap solutions injected simultaneously with the antigen (purified horse serum albumen) prevent anaphylactic shock.
5. The refractory state following anaphylactic shock is related in part to an increase in the antitryptic titer of the serum.
FURTHER EXPERIMENTS UPON THE EFFECTS OF EXTIRPATION OF THE THYMUS IN RATS, WITH SPECIAL REFERENCE TO THE ALLEGED PRODUCTION OF RACHITIC LESIONS
Authors: Pappenheimer Alwin M. 
Published: June 2004

Rachitic changes in the bones and teeth occur in young albino rats as the result of spontaneous disease, possibly of infective origin. This disease is often, but not always, accompanied by an arrest of growth and malnutrition.
There is no valid reason for attributing such lesions to the loss of thymic function. In some of the rats showing the disease, an unusual number of mitoses were found in the parathyroid glands, but no evidence of injury to these structures.
It has not been found possible to confirm the statements of Klose and Magnini as to the fatal effects of complete thymus extirpation in rats.
OBSERVATIONS ON EXPERIMENTAL TYPHOID INFECTION OF THE GALL BLADDER IN THE RABBIT
Authors: Nichols Henry J. 
Published: June 2004

1. Besredka's living sensitized vaccine, given intravenously, does not produce a typhoid lesion of the gall bladder in the rabbit.
2. The first transplant of this vaccine is capable of producing this lesion. Hence this vaccine is not entirely safe to handle.
3. Regular infections of the gall bladder have not been produced by carrying a known pathogenic strain on rabbit blood agar, by successive passage through animals, or by the use of freshly isolated strains.
4. No evidence could be demonstrated in the rabbit of the immunity produced in man by vaccination with a whole killed vaccine.
5. Vaccine treatment did not cure the gall bladder lesion.
6. With the present methods of producing infections in the chimpanzee and the rabbit, neither of these animals is suitable for deciding the problems of the immunization of man by vaccines. These problems must be settled, as some of them already have been settled, by actual experience with large numbers of men kept under close observation.
THE INHIBITION OF THE TOXICITY OF URANIUM NITRATE BY SODIUM CARBONATE, AND THE PROTECTION OF THE KIDNEY ACUTELY NEPHROPATHIC FROM URANIUM FROM THE TOXIC ACTION OF AN ANESTHETIC BY SODIUM CARBONATE
Authors: MacNider William Deb. 
Published: June 2004

1. The toxicity of uranium in animals of different ages is associated with the power of the metal to lead to the formation of organic acids, as, for instance, diacetic acid and also acetone.
2. The power of sodium carbonate to lessen the toxicity of uranium depends upon its power to delay the formation of such bodies and to cause their appearance in the urine in lessened amounts, and does not depend upon the power of the carbonate to detoxicate the metal.
3. The protection of the kidney by the carbonate, which is shown by the kidney being functionally much more active during an anesthesia than the kidney of a control animal, and by the Jack of fatty degeneration, acute swelling, and necrosis of the renal epithelium which is constantly seen in the unprotected kidneys, is probably dependent upon two factors: the neutralization of organic acids formed prior to and during the anesthesia, and the neutralization of hydrochloric acid which Graham has shown to be liberated by chloroform during an anesthesia induced by this substance.
INTRATESTICULAR IMPLANTATION OF THE FLEXNER-JOBLING RAT CARCINOMA
Authors: Woglom William H. 
Published: June 2004

The Flexner-Jobling adenocarcinoma of the rat is easily transplantable into the testis of this animal.
The resulting growths in the intact testis do not often attain the size of subcutaneous tumors.
The smaller size of intratesticular nodules can not be explained solely by the pressure to which they are subjected during their growth; other factors, which cannot be determined, appear to be concerned.
THE BACTERICIDAL PROPERTIES OF THE QUATERNARY SALTS OF HEXAMETHYLENETETRAMINE
Authors: Jacobs Walter A. , Heidelberger Michael , Bull Carroll G. 
Published: June 2004

The extension of the study of the quaternary salts of hexamethylenetetramine to those obtained by the addition of this base to the most varied types of substances containing aliphatically bound halogen has demonstrated that the introduction of the hexamethylenetetramine nucleus in this manner results in the production of bactericidal substances or enhances the bactericidal action if already present.
In particular it was found possible by the use of the halogenacetyl group, XCH2CO, as a connecting link, to furnish primary and secondary aliphatic and aromatic amines, alcohols, and hydrocarbons of the most varied character with the hexamethylenetetramine molecule and to study the relation between chemical constitution and bactericidal action in the series of substances so prepared. Because of the variety of chemical types studied, the results are too involved for a detailed summary here.
Many of the substances were found to be very powerful bactericides, and in a number of instances derivatives of purely aliphatic nature were found to possess an unusual bactericidal power.
Bacillus typhosus, streptococcus, meningococcus, and gonococcus were the microorganisms used for the tests, and striking instances of partial specificity were observed. This specificity was found to favor not one species alone, but instances were found in which each of the types of bacilli was shown to be especially susceptible to one or another of the particular types of compound employed. The source of this partial specificity is to be sought not in the hexamethylenetetramine nucleus itself but in the molecule to which it is attached.
The action of some of the substances was tested in the presence of serum or protein and was found to be not at all or only slightly inhibited. In other cases marked inhibition occurred. The factors controlling the serum- or protein-compatibility of these substances are likewise to be sought in that portion of the molecule other than the hexamethylenetetramine.
THE PROTECTION OF PATHOGENIC MICROORGANISMS BY LIVING TISSUE CELLS
Authors: Rous Peyton , Jones F. S. 
Published: June 2004

1. Living phagocytes are able to protect ingested organisms from the action of destructive substances in the surrounding fluid, and even from a strong homologous antiserum.
2. There is evidence that the protection by phagocytes is largely if not entirely conditioned on their being alive.
3. These facts should be taken into consideration in the study of diseases caused by infectious agents capable of living within tissue cells.
A comparative method for identification of gene structures and alternatively spliced variants
Authors: Chuang Trees-Juen , Chen Feng-Chi , Chou Meng-Yuan 
Published: June 2004

Abstract
Motivation: Alternative splicing (AS) serves as a mechanism to create diversity among functional proteins. Increasing evidence indicates that a large portion of genes have AS forms. Hence AS variants should be considered while analyzing gene structures.
Results: A new cross-species gene identification and AS analysis system, PSEP, has been developed. The system is based on expressed sequence tag (EST)-to-genome and genome-to-genome comparisons and is implemented in two steps: sequence alignment and a series of post-alignment processes, including progressive signal extraction and patching. For gene identification, these post-alignment processes serve as noise filters and enable PSEP to eliminate ∼88% of potential overprediction. The overall accuracy of PSEP is better than or comparable to that of other well-known cross-species gene prediction programs, including the ROSETTA program, TWINSCAN, SGP-1/-2 and SLAM, when tested on three benchmark datasets (the ELN gene region, the HoxA cluster and the ROSETTA set). In addition, 76.2 and 76.0% of multiple-exon genes in the ROSETTA dataset and human chromosome 20, respectively, are found to have AS forms. Approximately 23% of the 210 elementary alternatives identified in the ROSETTA dataset are not conserved between the human and mouse genomes, and none of the 210 transcripts is found in the RefSeq annotation. With its dual functions in cross-species conserved sequence analysis and AS analysis, PSEP is highly suitable for studying the evolution of AS patterns and for finding unidentified gene expression features.
Availability: The programs of PESP as well as the visualization tool required to build the proposed annotation scheme are available at ttp://www.sinica.edu.tw/~trees/PSEP/.
Developing optimal non-linear scoring function for protein design
Authors: Hu Changyu , Li Xiang , Liang Jie 
Published: June 2004

Abstract
Motivation. Protein design aims to identify sequences compatible with a given protein fold but incompatible to any alternative folds. To select the correct sequences and to guide the search process, a design scoring function is critically important. Such a scoring function should be able to characterize the global fitness landscape of many proteins simultaneously.
Results: To find optimal design scoring functions, we introduce two geometric views and propose a formulation using a mixture of non-linear Gaussian kernel functions. We aim to solve a simplified protein sequence design problem. Our goal is to distinguish each native sequence for a major portion of representative protein structures from a large number of alternative decoy sequences, each a fragment from proteins of different folds. Our scoring function discriminates perfectly a set of 440 native proteins from 14 million sequence decoys. We show that no linear scoring function can succeed in this task. In a blind test of unrelated proteins, our scoring function misclassfies only 13 native proteins out of 194. This compares favorably with about three–four times more misclassifications when optimal linear functions reported in the literature are used. We also discuss how to develop protein folding scoring function.
Availability: Available on request from the authors.
Comparison of probabilistic combination methods for protein secondary structure prediction
Authors: Liu Yan , Carbonell Jaime , Klein-Seetharaman Judith , Gopalakrishnan Vanathi 
Published: June 2004

Abstract
Motivation: Protein secondary structure prediction is an important step towards understanding how proteins fold in three dimensions. Recent analysis by information theory indicates that the correlation between neighboring secondary structures are much stronger than that of neighboring amino acids. In this article, we focus on the combination problem for sequences, i.e. combining the scores or assignments from single or multiple prediction systems under the constraint of a whole sequence, as a target for improvement in protein secondary structure prediction.
Results: We apply several graphical chain models to solve the combination problem and show that they are consistently more effective than the traditional window-based methods. In particular, conditional random fields (CRFs) moderately improve the predictions for helices and, more importantly, for beta sheets, which are the major bottleneck for protein secondary structure prediction.