bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bivartect: accurate and memory-saving breakpoint detection by direct read comparison
Authors: Shimmura Keisuke , Kato Yuki , Kawahara Yukio 
Published: January 2020

Abstract

Motivation
Genetic variant calling with high-throughput sequencing data has been recognized as a useful tool for better understanding of disease mechanism and detection of potential off-target sites in genome editing. Since most of the variant calling algorithms rely on initial mapping onto a reference genome and tend to predict many variant candidates, variant calling remains challenging in terms of predicting variants with low false positives.

Results
Here we present Bivartect, a simple yet versatile variant caller based on direct comparison of short sequence reads between normal and mutated samples. Bivartect can detect not only single nucleotide variants but also insertions/deletions, inversions and their complexes. Bivartect achieves high predictive performance with an elaborate memory-saving mechanism, which allows Bivartect to run on a computer with a single node for analyzing small omics data. Tests with simulated benchmark and real genome-editing data indicate that Bivartect was comparable to state-of-the-art variant callers in positive predictive value for detection of single nucleotide variants, even though it yielded a substantially small number of candidates. These results suggest that Bivartect, a reference-free approach, will contribute to the identification of germline mutations as well as off-target sites introduced during genome editing with high accuracy.

Availability and implementation
Bivartect is implemented in C++ and available along with in silico simulated data at https://github.com/ykat0/bivartect.

Supplementary information
Supplementary data are available at Bioinformatics online.
Chronic testicular Chlamydia muridarum infection impairs mouse fertility and offspring development†
Authors: Bryan Emily R , Redgrove Kate A , Mooney Alison R , Mihalas Bettina P , Sutherland Jessie M , Carey Alison J , Armitage Charles W , Trim Logan K , Kollipara Avinash , Mulvey Peter B M , Palframan Ella , Trollope Gemma , Bogoevski Kristofor , McLachlan Robert , McLaughlin Eileen A , Beagley Kenneth W 
Published: January 2020

AbstractWith approximately 131 million new genital tract infections occurring each year, Chlamydia is the most common sexually transmitted bacterial pathogen worldwide. Male and female infections occur at similar rates and both cause serious pathological sequelae. Despite this, the impact of chlamydial infection on male fertility has long been debated, and the effects of paternal chlamydial infection on offspring development are unknown. Using a male mouse chronic infection model, we show that chlamydial infection persists in the testes, adversely affecting the testicular environment. Infection increased leukocyte infiltration, disrupted the blood:testis barrier and reduced spermiogenic cell numbers and seminiferous tubule volume. Sperm from infected mice had decreased motility, increased abnormal morphology, decreased zona-binding capacity, and increased DNA damage. Serum anti-sperm antibodies were also increased. When both acutely and chronically infected male mice were bred with healthy female mice, 16.7% of pups displayed developmental abnormalities. Female offspring of chronically infected sires had smaller reproductive tracts than offspring of noninfected sires. The male pups of infected sires displayed delayed testicular development, with abnormalities in sperm vitality, motility, and sperm-oocyte binding evident at sexual maturity. These data suggest that chronic testicular Chlamydia infection can contribute to male infertility, which may have an intergenerational impact on sperm quality.
Protocoled thrombolytic therapy for frostbite improves phalangeal salvage rates
Authors: Paine Rosemary Elizabeth , Turner Elizabeth Noel , Kloda Daniel , Falank Carolyne , Chung Bruce , Carter Damien Wilson 
Published: January 2020

Abstract

Background
Frostbite is a cold injury that has the potential to cause considerable morbidity and long-term disability. Despite the complexity of these patients, diagnostic and treatment practices lack standardization. Thrombolytic therapy has emerged as a promising treatment modality, demonstrating impressive digit salvage rates. We review our experience with thrombolytic therapy for severe upper extremity frostbite.

Methods
Retrospective data on all frostbite patients evaluated at our institution from December 2017 to March 2018 was collected. A subgroup of patients with severe frostbite treated with intra-arterial thrombolytic therapy (IATT) were analysed.

Results
Of the 17 frostbite patients treated at our institution, 14 (82%) were male and the median age was 31 (range: 19–73). Substance misuse was involved in a majority of the cases (58.8%). Five (29.4%) patients with severe frostbite met inclusion criteria for IATT and the remaining patients were treated conservatively. Angiography demonstrated a 74.5% improvement in perfusion after tissue plasminogen activator thrombolysis. When comparing phalanges at risk on initial angiography to phalanges undergoing amputation, the phalangeal salvage rate was 83.3% and the digit salvage rate was 80%. Complications associated with IATT included groin hematoma, pseudoaneurysm and retroperitoneal hematoma.

Conclusions
Thrombolytic therapy has the potential to greatly improve limb salvage and functional recovery after severe frostbite when treated at an institution that can offer comprehensive, protocoled thrombolytic therapy. A multi-center prospective study is warranted to elucidate the optimal treatment strategy in severe frostbite.
Colorimetric Determination of Blood Arginase
Authors: Friedman Max M , Becker Edythe 
Published: January 2020

Abstract
A colorimetric procedure for blood arginase has been described, based on hemolyzing the red blood cells with saponin and determining the urea formed by action of the enzyme on an arginine substrate.
The range of blood arginase in a series of normal human subjects has been presented.
Cross-Contaminator Exclusion Test for Dry-Ashing Determination of Protein-Bound Iodine
Authors: Samson Mayer , Brown Herman , Eichen Seymour 
Published: January 2020

Abstract
A simple qualitative test for iodine in blood serum has been described. It is designed to detect sera which are potential cross-contaminators in dry-ashing PBI procedures. One drop of serum is used. Added operating time in a PBI series of 20-40 determinations is not over 30 minutes.
A Note on Quantitative Urobilinogen Determinations
Authors: Balikov Bernard 
Published: January 2020

Abstract
In the article, "A Note on Quantitative Urobilinogen Determinations", by Bernard Balikov, Vol. 1, 264 (August 1955), the abscissa label of Fig. 1, page 265, should read "2% glacial acetic acid assumed to yield 100% recovery."
Studies of Body Water and Water Turnover Determined with Deuterium Oxide Added to Food
Authors: Gaebler O H , Choitz H C 
Published: January 2020

Abstract
In 5 dogs which ingested 25 or 50 ml. of D2O with one daily meal, maximal plasma concentrations of tracer were reached in 12-24 hr. The disappearance rate during 14 days was exponential, confirming studies of others in humans. Water turnover, calculated from values obtained for body water and the disappearance rates, agreed well with total water intake, which included water taken as such and that derived by oxidation. Water intake per square meter of surface area varied widely; there was also no constant relationship between either total turnover or extrarenal loss and caloric intake. Since animals were maintained at nearly constant weights for long periods, caloric intake and total heat production were presumably equivalent. Thus the possibility of estimating total heat production from water turnover or extrarenal loss was not promising, but the validity of body water and turnover estimations was well supported. Average value for body water was 60.6% of body weight, with a range of 56.1% to 66.6%.
A Simple Serum Iron Method Using the New Sensitive Chromogen Tripyridyl-s-triazine
Authors: Fischer David S , Price David C 
Published: January 2020

Abstract
A simple, specific and reproducible serum iron method is described using the recently synthesized and highly sensitive chromogen, tripyridyl-S-triazine. The absorbance of this chromogen is compared to other iron reagents. Procedural modifications are given for using the Ramsay iron-binding capacity method with this serum iron procedure. The normal values found agree with most of those in the literature which has been reviewed.
Multiple Automatic Sequential Analysis
Authors: Skeggs Leonard T , Hochstrasser Harry 
Published: January 2020

Abstract
A multiple automatic analyzer has been constructed which determines albumin, total protein, chloride, carbon dioxide, sodium, potassium, glucose, and urea nitrogen. The results for each of these 8 determinations are obtained in sequence for an individual sample and are recorded on a single sheet of paper. The entire system is calibrated by means of a standard solution containing all 8 of the components under test. Results appear on the record in a directly readable and immediately usable form. The actual record is used as the laboratory report sent to the requesting physician.
Interference of Thiouracil in the Ferric Chloride-Sulfuric Acid Cholesterol Reaction
Authors: Rice Eugene W 
Published: January 2020

Abstract
Thiouracil, previously recommended as a preservative to be added to serum for butanol-extractable iodine determinations, inhibits the ferric chloride-sulfuric acid color reaction for cholesterol. The color inhibition may be eliminated by shaking the serum for about 5 min. with solid silver iodate prior to cholesterol analysis.
Spectrophotometric Determination of Magnesium in Blood Serum Using Magon
Authors: Burcar Patricia J , Boyle Albert J , Mosher Robert E 
Published: January 2020

Abstract
A spectrophotometric method for the determination of serum magnesium using Magon, 1-azo-2-hydroxy-3- (2,4-dimethylcarboxanilido) naphthalene- 1’- (2-hydroxybenzene), is presented. The serum is prepared by a nitric-perchloric acid digestion. Interfering phosphate is removed as aluminum phosphate. The colored complex is developed at pH 11.2 in an alcoholic medium and read at 505 mµ.
Preservation of Blood Ammonia by Rapid Freezing-A Method for Delayed Determinations
Authors: Orloff Marshall J , Stevens Clarence O 
Published: January 2020

Abstract
A method is described for preservation of blood for delayed determinations of ammonia by rapid freezing of the samples in a dry ice and acetone solution followed by storage of the specimens in the frozen state. The method was evaluated by first establishing the reproducibility of the chemical method used for blood ammonia analysis in 714 consecutive samples of dog blood which were analyzed in duplicate, and then determining whether freezing caused greater changes in ammonia concentration than one would expect knowing the reproducibility of the chemical method. Studies in 200 samples of dog blood with ammonia levels of 16 to 2904 µg./100 ml., each of which was analyzed immediately and after 24 hr. of freezing, showed that freezing and storage for 24 hr. did not significantly affect the blood ammonia content. Studies of 22 samples of frozen dog blood with ammonia levels of 11 to 2624 µg/100 ml., parts of each of which were analyzed daily for 5 consecutive days, showed that storage in the frozen state for up to 72 hr. had no significant effect on the ammonia concentration, but that storage for 96 hr. or longer resulted in increases in blood ammonia beyond acceptable limits. It is concluded that accurate delayed measurements of blood ammonia may be accomplished by rapid freezing of the blood immediately after shedding, and storage of the frozen samples for up to 72 hr.
Urea Synthesis by Hemic Cells
Authors: Moore W Tabb , Rodarte Joseph , Smith Lloyd H 
Published: January 2020

Abstract
A method for measuring urea production by isolated erythrocytes and leucocytes under physiologic conditions is described. Erythrocytes from 10 normal subjects formed an average of 82.5 mµmoles urea/ml. packed cells/hr. Leucocytes formed 7.4 mµmoles urea/108 cells/hr. By extrapolation, total urea synthesis by circulating erythrocytes would be approximately 270 mg./day and by the granulocyte pool approximately 5 mg./day. The total contribution of circulating hemic cells to over-all urea synthesis approximates 1 to 3% on an average protein diet. Six patients with cystinuria were also studied. No defect in urea synthesis, as a reflection of impaired arginine transport, could be detected in their blood cells with the conditions employed.
A Quantitative Assay for Urinary Porphobilinogen
Authors: Moore Donald J , Labbe Robert F 
Published: January 2020

Abstract
A procedure has been developed for the rapid, quantitative determination of urinary porphobilinogen. Interfering substances are removed by selectively adsorbing the porphobilinogen with an ion-exchange resin using a batch method. After acid elution of the porphobilinogen, Ehrlich's reagent is added to produce the chromophore, which is then measured spectrophotometrically. Obtaining absorption at two wavelengths permits a differentiation of porphobilinogen from interfering reactants not removed by the resin treatment. This assay is relatively simple, dependable, highly reproducible for increased amounts, and more specific than the qualitative assay.
Quantitation of Serum Urea as Microcapillary Columns of Dixanthylurea
Authors: Searcy R L , Korotzer J L , Douglas G L , Bergquist L M 
Published: January 2020

Abstract
A simple technic is proposed for direct estimation of urea in terms of columns of dixanthylurea precipitated from serum. The procedure is reproducible and yields results comparable to those obtained colorimetrically using normal and uremic sera. An equation has been derived which permits conversion of levels of dixanthylurea columns, in millimeters, to urea nitrogen concentrations. The new method is useful in detecting as well as monitoring cases of uremia.
Comparison of Enzyme Activities of Arterial Samples from Sexually Mature Men and Women
Authors: Kirk John Esben 
Published: January 2020

Abstract
A comparison was made of activities of 25 different enzymes in aortic, pulmonary artery, and coronary artery samples derived from 18- to 54-year-old men and women. The aorta and coronary artery of women were found to contain lower concentrations of 4 TPN-dependent enzymes (glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, isocitric dehydrogenase, and TPN-malic enzyme). Since TPNH is a compound involved in the synthesis of cholesterol and fatty acids, the observed sex difference in arterial TPN-dependent enzyme activities may be associated with the lower susceptibility of premenopausal women to arteriosclerosis.
Studies on the Determination of Bile Pigments
Authors: Stevenson G W , Jacobs S L , Henry R J 
Published: January 2020

Abstract
The absorbance at 450 mµ of serum diluted with acidified ethylene glycol is used as a measure of the serum's total bilirubin content in a single-tube, single-extraction method for rapid determination of free and total bilirubin in 0.1 ml. of serum. With the addition of chloroform, free bilirubin is extracted into the chloroform but conjugated bilirubin remains in the ethylene glycol. Free bilirubin is determined from the absorbance at 450 mµ in the chloroform layer. Conjugated bilirubin is calculated from the difference. Absorbance readings at 520 mµ compensate for the absorbance at 450 mµ, due to hemoglobin in the serum. Comparison with the Malloy-Evelyn procedure showed equivalent levels of total but higher levels of conjugated bilirubin.
A Diagnostic Test for Fructosuria
Authors: Sarma P L 
Published: January 2020

Abstract
As little as 8 µg fructose can be identified by the red or yellow color produced by adding 2 drops of a fructose solution to approximately 0.2 gm. of potassium hydroxide on a spot plate. Glucose interferes with this test only when less than 0.1 mg. of fructose is present in a mixture of more than 0.9 mg. of glucose. This test may be used for a rapid diagnosis of fructosuria if 0.5% or more of fructose is excreted in the urine.
A Comparison of Some Methods of Cholesterol Measurement
Authors: Hawthorne Betty E 
Published: January 2020

Abstract
Five referee sera were analyzed for total cholesterol at several laboratories by up to 10 different methods or modifications. Results by any method varied less within a single laboratory than among laboratories, although the ranges of replicate analyses reported differed considerably. Those methods including procedures for saponification with potassium hydroxide and some isolation of cholesterol from other chromogens by digitonin precipitation or re-extraction into petroleum ether, in general, yielded results somewhat lower than those obtained by methods which did not include these procedures.
A Simplified Technique for Determination of Small Amounts of Calcium as Oxalate
Authors: Van Slyke Donald D , Carson Paul E 
Published: January 2020

Abstract
Procedures for determination of calcium by oxalate precipitation are reviewed, and a method is described in which the calcium oxalate precipitate is both formed and washed in a filter tube with a fritted-glass filter. Washing with saturated calcium oxalate solution is completed in 1-2 min. The washed precipitate is redissolved in perchloric acid solution and the dissolved oxalate is either titrated or determined manometrically by the CO2 evolved from oxidation with ceric sulfate.
Rapid Determination of Plasma Ammonia by an Ion-Exchange Technic
Authors: Forman Donald T 
Published: January 2020

Abstract
A method is described for the colorimetric determination of ammonia in plasma by a batch ion-exchange procedure. The method combines separation of ammonium ion, using a strongly acidic cation-exchange resin, with a sensitive colorimetric procedure which simultaneously elutes and colorimetrically reacts with the ammonium ion to produce a stable color.
Interference by basic amino acids is negligible, and the great sensitivity of the color reaction permits the measurement of ammonia of the order of 0.5 µg./ml. The effects of variations in the experimental conditions are examined, and the results of recovery experiments and other tests of precision and accuracy are reported. In comparison with other methods in current use, this method has distinct advantages in sensitivity, simplicity, and rapidity of determination, provided the conditions and methods of measurement are controlled carefully.
Effect of Toluene and Similar Compounds on the Carbohydrate-Anthrone Reaction
Authors: Devor Arthur W , Baker William L , Devor Kenneth A 
Published: January 2020

Abstract
Toluene interferes with the anthrone reaction for hexoses causing a decrease in the absorption maximum at 625 mµ and producing a second absorption band with a maximum at 475 mµ. Xylene, benzene, and cyclohexene also interfere, whereas cyclohexane, o-chlorobenzene, and benzoic acid do not.
Decolorization on Freezing of Ferricyanide-Cyanide Solution used for Hemoglobin Determinations
Authors: Mickelsen Olaf , Woolard Helen , Ness Arthur T 
Published: January 2020

Abstract
When Drabkin's solution (used for the determination of hemoglobin), which contains K3Fe(CN)6, KCN, and NaHCO3, is frozen, it loses its greenish-yellow color. The solution remains colorless even after thawing. The reaction, for which there is no satisfactory explanation, involves the reduction of the K3Fe(CN)6 to K4Fe(CN)6, with KCN being oxidized to KCNO.
Serum Glycoproteins and Seromucoid in Patients with Myocardial Infarction
Authors: Keyser J W , Stephens B T 
Published: January 2020

Abstract
Seromucoid and serum total glycoproteins were measured in 7 patients with myocardial infarction. In all cases the highest concentrations of these proteins were reached several days after the concentration of glutamic-oxalacetic transaminase had begun to return to normal. In 2 cases paper electrophoretic analysis of the serum proteins was performed. A rise in the concentration of 1- and 2-globulins occurred after infarction, and PAS staining indicated that the rise in total glycoprotein was largely or entirely accounted for by these two fractions. The concentration of serum albumin fell considerably after infarction, reaching a minimum at about 6 days; - and -globulin concentrations appeared to fall slightly. In general, the presence of C-reactive protein corresponded roughly with the period during which the seromucoid concentration was elevated. It is suggested that the elevation of seromucoid and total glycoproteins represents a nonspecific response to the tissue injury.
Bovine Serum Ultrafiltrate as a General Standard in Clinical Chemical Analysis
Authors: Saifer Abraham , Deutscher Claire 
Published: January 2020

Abstract
This survey has shown some facts of considerable interest to the clinical chemist.
First, it is evident that bovine blood serum ultrafiltrate constitutes one of the best general standards so far developed for clinical chemical control analysis. It is a stable product that can be prepared in large lots and kept for relatively long periods of time by storage in a refrigerator. Such a standard will be extremely useful in clinical chemical laboratories in the standardization of their technics and as an aid in the elimination of systematic errors of analysis and in routine laboratory control. On the other hand, the absence of serum proteins and sterols precludes the use of this standard for the analysis of these constituents. The second fact that emerges from this survey is that errors in clinical chemical analysis still occur. The finding that individual results from selected laboratories have been in error, imposes the obligation of periodic control checkups by the chemist charged with the supervision of the laboratory.
Finally, a general standard of this sort permits an exhaustive comparison of different methods for any given constituent without fear of variation from sample to sample.
Serum Globulin Fractions in Chronic Rheumatic Diseases
Authors: Salt Harold B 
Published: January 2020

Abstract
Investigations into the serum protein patterns that occur in chronic rheumatic diseases, formerly made by salt-fractionation methods, are now revised with the aid of the superior technic of microelectrophoretic separation.
Using the microelectrophoretic method, supplemented by a single salt-fractionation procedure, the concentrations of albumin, α1-globulin, α2-globulin, β-globulin and γ-globulin in the sera of 26 patients variously affected by chronic rheumatic diseases were determined.
Normal protein patterns were found in all the 12 sera with normal total globulin content, whereas variously abnormal protein patterns were found in all of the 14 hyperglobulinemic sera.
The hyperglobulinemia of chronic rheumatic diseases was found most frequently to be due to increments in γ-globulin, often accompanied also by increases in α2-globulin. Less frequently, increased amounts of β-globulin were found, and in some cases an elevation of α1-globulin. These abnormalities were all detectable electrophoretically, whereas the method for the salting-out of γ-globulin was unsatisfactory.
Yeast Adenylic Acid as a Substrate for Serum Acid Phosphatase
Authors: Reynolds Orland B , Reynolds Moira Davison , Walker Burnham S 
Published: January 2020

Abstract
Yeast adenylic acid was investigated as a substrate for serum acid phosphatase determination. It was compared as a substrate primarily with β-glycerophosphate and found to be very similar in selectivity and sensitivity. There appears to be no significant advantage in the use of yeast adenylic acid over β-glycerophosphate for this purpose.