bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast comparison of DNA sequences by oligonucleotide profiling
Authors: Arnau Vicente , Gallach Miguel , Marín Ignacio 
Published: August 2008

Abstract

Background
The comparison of DNA sequences is a traditional problem in genomics and bioinformatics. Many new opportunities emerge due to the improvement of personal computers, allowing the implementation of novel strategies of analysis.

Findings
We describe a new program, called UVWORD, which determines the number of times that each DNA word present in a sequence (target) is found in a second sequence (source), a procedure that we have called oligonucleotide profiling. On a standard computer, the user may search for words of a size ranging from k = 1 to k = 14 nucleotides. Average counts for groups of contiguous words may also be established. The rate of analysis on standard computers is from 3.4 (k = 14) to 16 millions of words per second (1 ≤ k ≤ 8). This makes feasible the fast screening of even the longest known DNA molecules.

Discussion
We show that the combination of the ability of analyzing words of relatively long size, which occur very rarely by chance, and the fast speed of the program allows to perform novel types of screenings, complementary to those provided by standard programs such as BLAST. This method can be used to determine oligonucleotide content, to characterize the distribution of repetitive sequences in chromosomes, to determine the evolutionary conservation of sequences in different species, to establish regions of similar DNA among chromosomes or genomes, etc.
Prediction of protein secondary structures with a novel kernel density estimation based classifier
Authors: Chang Darby Tien-Hao , Ou Yu-Yen , Hung Hao-Geng , Yang Meng-Han , Chen Chien-Yu , Oyang Yen-Jen 
Published: August 2008

Abstract

Background
Though prediction of protein secondary structures has been an active research issue in bioinformatics for quite a few years and many approaches have been proposed, a new challenge emerges as the sizes of contemporary protein structure databases continue to grow rapidly. The new challenge concerns how we can effectively exploit all the information implicitly deposited in the protein structure databases and deliver ever-improving prediction accuracy as the databases expand rapidly.

Findings
The new challenge is addressed in this article by proposing a predictor designed with a novel kernel density estimation algorithm. One main distinctive feature of the kernel density estimation based approach is that the average execution time taken by the training process is in the order of O(nlogn), where n is the number of instances in the training dataset. In the experiments reported in this article, the proposed predictor delivered an average Q3 (three-state prediction accuracy) score of 80.3% and an average SOV (segment overlap) score of 76.9% for a set of 27 benchmark protein chains extracted from the EVA server that are longer than 100 residues.

Conclusion
The experimental results reported in this article reveal that we can continue to achieve higher prediction accuracy of protein secondary structures by effectively exploiting the structural information deposited in fast-growing protein structure databases. In this respect, the kernel density estimation based approach enjoys a distinctive advantage with its low time complexity for carrying out the training process.
Norepinephrine to increase blood pressure in endotoxaemic pigs is associated with improved hepatic mitochondrial respiration
Authors: Regueira Tomas , Bänziger Bertram , Djafarzadeh Siamak , Brandt Sebastian , Gorrasi Jose , Takala Jukka , Lepper Philipp M , Jakob Stephan M 
Published: August 2008

Abstract
Introduction
Low blood pressure, inadequate tissue oxygen delivery and mitochondrial dysfunction have all been implicated in the development of sepsis-induced organ failure. This study evaluated the effect on liver mitochondrial function of using norepinephrine to increase blood pressure in experimental sepsis.

Methods
Thirteen anaesthetized pigs received endotoxin (Escherichia coli lipopolysaccharide B0111:B4; 0.4 μg/kg per hour) and were subsequently randomly assigned to norepinephrine treatment or placebo for 10 hours. Norepinephrine dose was adjusted at 2-hour intervals to achieve 15 mmHg increases in mean arterial blood pressure up to 95 mmHg. Systemic (thermodilution) and hepatosplanchnic (ultrasound Doppler) blood flow were measured at each step. At the end of the experiment, hepatic mitochondrial oxygen consumption (high-resolution respirometry) and citrate synthase activity (spectrophotometry) were assessed.

Results
Mean arterial pressure (mmHg) increased only in norepinephrine-treated animals (from 73 [median; range 69 to 81] to 63 [60 to 68] in controls [P = 0.09] and from 83 [69 to 93] to 96 [86 to 108] in norepinephrine-treated animals [P = 0.019]). Cardiac index and systemic oxygen delivery (DO2) increased in both groups, but significantly more in the norepinephrine group (P < 0.03 for both). Cardiac index (ml/min per·kg) increased from 99 (range: 72 to 112) to 117 (110 to 232) in controls (P = 0.002), and from 107 (84 to 132) to 161 (147 to 340) in norepinephrine-treated animals (P = 0.001). DO2 (ml/min per·kg) increased from 13 (range: 11 to 15) to 16 (15 to 24) in controls (P = 0.028), and from 16 (12 to 19) to 29 (25 to 52) in norepinephrine-treated animals (P = 0.018). Systemic oxygen consumption (systemic VO2) increased in both groups (P < 0.05), whereas hepatosplanchnic flows, DO2 and VO2 remained stable. The hepatic lactate extraction ratio decreased in both groups (P = 0.05). Liver mitochondria complex I-dependent and II-dependent respiratory control ratios were increased in the norepinephrine group (complex I: 3.5 [range: 2.1 to 5.7] in controls versus 5.8 [4.8 to 6.4] in norepinephrine-treated animals [P = 0.015]; complex II: 3.1 [2.3 to 3.8] in controls versus 3.7 [3.3 to 4.6] in norepinephrine-treated animals [P = 0.09]). No differences were observed in citrate synthase activity.

Conclusion
Norepinephrine treatment during endotoxaemia does not increase hepatosplanchnic flow, oxygen delivery or consumption, and does not improve the hepatic lactate extraction ratio. However, norepinephrine increases the liver mitochondria complex I-dependent and II-dependent respiratory control ratios. This effect was probably mediated by a direct effect of norepinephrine on liver cells.
Differential temporal profile of lowered blood glucose levels (3.5 to 6.5 mmol/l versus 5 to 8 mmol/l) in patients with severe traumatic brain injury
Authors: Meier Regula , Béchir Markus , Ludwig Silke , Sommerfeld Jutta , Keel Marius , Steiger Peter , Stocker Reto , Stover John F 
Published: August 2008

Abstract
Introduction
Hyperglycaemia is detrimental, but maintaining low blood glucose levels within tight limits is controversial in patients with severe traumatic brain injury, because decreased blood glucose levels can induce and aggravate underlying brain injury.

Methods
In 228 propensity matched patients (age, sex and injury severity) treated in our intensive care unit (ICU) from 2000 to 2004, we retrospectively evaluated the influence of different predefined blood glucose targets (3.5 to 6.5 versus 5 to 8 mmol/l) on frequency of hypoglycaemic and hyperglycaemic episodes, insulin and norepinephrine requirement, changes in intracranial pressure and cerebral perfusion pressure, mortality and length of stay on the ICU.

Results
Mortality and length of ICU stay were similar in both blood glucose target groups. Blood glucose values below and above the predefined levels were significantly increased in the 3. 5 to 6.5 mmol/l group, predominantly during the first week. Insulin and norepinephrine requirements were markedly increased in this group. During the second week, the incidences of intracranial pressure exceeding 20 mmHg and infectious complications were significantly decreased in the 3.5 to 6.5 mmol/l group.

Conclusion
Maintaining blood glucose within 5 to 8 mmol/l appears to yield greater benefit during the first week. During the second week, 3.5 to 6.5 mmol/l is associated with beneficial effects in terms of reduced intracranial hypertension and decreased rate of pneumonia, bacteraemia and urinary tract infections. It remains to be determined whether patients might profit from temporally adapted blood glucose limits, inducing lower values during the second week, and whether concomitant glucose infusion to prevent hypoglycaemia is safe in patients with post-traumatic oedema.
Human dendritic cell line models for DC differentiation and clinical DC vaccination studies
Authors: Santegoets Saskia J A M , van den Eertwegh Alfons J M , van de Loosdrecht Arjan A , Scheper Rik J , de Gruijl Tanja D 
Published: July 2008

AbstractDendritic cells (DC) are increasingly applied in the immunotherapy of cancer. As the development of a standardized DC vaccine product is often hampered by the limited availability of DC precursors and inter- and intra-donor variability, and the preparation of individual vaccines is labor-intensive, it would be preferable to use DC from a readily available and unlimited source, such as cell lines can provide. It has been described that leukemia-derived cell lines are able to differentiate into functional DC, creating possibilities for the development of highly reproducible DC vaccines and providing in vitro model systems for in-depth studies about DC physiology. This review discusses the different human DC cell line differentiation models described so far. Based on the available data, characteristics that determine the ability of leukemia cells to differentiate along the different precursor stages into functional DC will be formulated. In addition, evidence will be provided that the human CD34+ acute myeloid leukemia cell line MUTZ-3 provides DC that exhibit the functional properties that are crucial for the in vivo generation of CTL-mediated immunity and thus, currently, represents the most valuable, sustainable model system for myeloid DC differentiation and clinical DC vaccination studies.
The Action of Neurotic Medicines in Insanity: Being “Observations and Experiments on the Use of Opium, Bromide of Potassium, and Cannabis Indica in Insanity, especially in regard to the effects of the two latter given separately”
Authors: Clouston T. S. 
Published: August 2008

The following is an abstract of the above paper. It begins by saying that :—So many cases of insanity consist of simple brain excitement, and in so many more is excitement the most distressing symptom, that if we could discover any agent which would subdue this excitement, and at the same time not interfere with the improved nutrition of the brain which rest, tonics, and good diet will effect, and on which complete recovery of its normal functions depends, such an agent would be a most incalculable blessing. There are many cases in which a physician knows that if he could tide over his patient for a few weeks of excitement, recovery would come as the natural termmination of the attack. Much distruct of strong narcotics prevails among the profession since Dr. Anstie's work on “Stimulants and Narcotics” appeared. And yet how is such a case of maniacal excitement to be managed without them out of a lunatic asylum? The exact condition of the brain cells in mania being as yet quite unknown, we cannot apply a direct antidote. At best we can only work empirically. But our empiricism may be founded on a rational and scientific examination of the effects of the drugs we use, and the natural history of the disease we treat, or it may be a mere haphazard employment of some agent recommended by some one who had no rational ground for his recommendation at all.
The Heating, Ventilation, and Electric Lighting of the Hospital at the Montrose Royal Asylum
Authors: Howden James 
Published: August 2008

In connection with the description of the new hospital in the Journal of Mental Science for January, 1889, I have now to add a detailed account of the heating, ventilation, and electric lighting as now completed.The heating and ventilation are effected by steam on the low pressure principle, by which all the condensed water is returned into the boilers by its own gravity.
Stuporose Insanity Consecutive to Induced Hypnotism
Authors: Nolan M. J. 
Published: August 2008

“Je n'ai jamais rien vu survenir de grave”∗ wrote M. Richet to Professor Heidenhain, giving the results of the experiments he had made in hypnotism; and no doubt he was fully justified in doing so, since only one individual tested by him suffered any inconvenience, and that in a very slight and passing degree. Putting this evidence with his own observations, Heidenhain not unnaturally asserts that “there is no ground whatever for objection to hypnotic experiments,” † and again he says “it must be remembered that the necessity for precaution has not arisen as the result of unfavourable experience, but merely because it is our duty, for the sake of the person experimented on, to be over careful rather than not careful enough.” † The case under present consideration is, however, calculated to shake our confidence in such assurances of complete immunity from danger in hypnotic experiments, especially when conducted by unskilled persons; and indicates, moreover, that Professors Richet and Heidenhain owe their happy results as much to good fortune as to theperfect freedom from risk they calculate on with so much certainty. Still further, it confirms the remarks of Binet and Féré, who say “with respect to the performance of such experiments in public, it should be condemned just as we condemn public dissections of the dead body, and vivisection in public.”∗ But this note of warning, though important, is perhaps the least interesting of the many considerations to which a study of this case gave rise, since it was particularly rich in the various psychological and physiological manifestations appertaining to the hypnotic and stuporose states. For this reason I desire to bring it under notice, and, owing to the kindness of my chief, Dr. Conolly Norman, who placed the man under my immediate charge for observations and treatment, I am enabled to do so. My grateful acknowledgments are also due to Surgeon-Major Martin, A.M.S., who kindly furnished me with the notes made by him on the patient's condition during his period of treatment at the Royal Infirmary, Dublin, prior to his removal to this asylum.
Lunacy Administration in Berlin and in Scotland, with Special Reference to the Care of the Insane in Private Dwellings
Authors: Sibbald John 
Published: August 2008

The Supervision and Management of the Patients in Private Dwellings.The way in which the boarding-out system is administered at Berlin is the result of experience. Its present form differs in some respects from the arrangements made at the commencement of the experiment. It is unnecessary to describe the gradual evolution of the system, the way in which cumbrous regulations were eliminated, and in which greater efficiency was given to the arrangements; but it is proper to recognize the great capacity as an administrator which has been shown by Dr. Sander, to whom, as director of the asylum, the development of the system has been chiefly due.
Medico-Legal Cases
Authors: Mercier  
Published: August 2008

[The Editors request that Members will oblige by sending full newspaper reports of all cases of interest as published by the local press at the time of the Assizes.]Reg. v. Coombes.—“The Plaistow Murder.”Robert Allen Coombes, 13, was indicted for the wilful murder of his mother. The facts, which were not disputed, were of a very revolting character. The prisoner and his younger brother, Nathaniel, æt. 12, had for some days discussed the murder of their mother, who appears to have treated the boys not unkindly. On July 4th prisoner purchased a knife and concealed it. Early on the moraine of the 8th he stabbed his mother twice with it while she was in bed. He had slept with his mother, and said that she had punched him during the night. He took money from his mother's purse, and accounted for his possession of it and for her disappearance by a series of ingenious and elaborate lies. He wrote a letter to the cashier of the company in whose employment his father was, asking for money on the ground of his mother's illness, and backed up the application with an old medical certificate, from which he tore the date. He wrote another letter to his father, in which he accounted for his mother not writing by saying she had hurt her hand. He also wrote an advertisement for an evening paper, asking for a loan of £30. The two boys agreed that the elder should stab their mother when the younger gave a signal by coughing twice. On the morning of the murder and after the crime they went together to Lord's Cricket Ground.
The Treatment of Melancholia by the Lactic Acid Bacillus
Authors: Phillips J. George Porter 
Published: August 2008

Melancholia, with its attendant constipation and faulty alimentation, lends itself at once to a dietetic form of treatment.Whether the constipation is dependent on defective innervation and is a direct symptom of melancholia or is the initial cause of this mental disturbance, it matters not so far as our endeavours in treatment are concerned.
A Case of “Status Epilepticus” and Death due to Cerebral Cysts of Cysticercus Cellulosæ (Larvæ of Tænia solium)
Authors: Peachell G. E. 
Published: August 2008

As this is a fairly rare condition, the following case is considered worth publishing:R. P—, æt. 39, married, a private in the R.F.A., was admitted to the Isle of Wight County Asylum on January 2nd, 1915, from a Red Cross Hospital in a condition of status epilepticus. The history obtained from his wife was interesting. He joined the Army when about 18, and spent six years in India. He took part in the South African War for fifteen months. He returned to England in 1903, married, and had several healthy children, and had lived at Dorchester for the last ten years. At the outbreak of war he was called up on the Reserve, and sent to France with the B.E.F., and was in the battle of the Aisne. Early in October he developed “epilepsy,” and was invalided to England. He had always been strong and healthy till then, and never had a fit previously. Under treatment he improved, and was on sick furlough, when in November he had a severe epileptic attack, and was readmitted to a military hospital. He then became sullen, drowsy, and irritable, with occasional slight fits till December 20th, when he had three severe attacks, but came round from them, and was able to write a clear letter to his wife on December 26th. On January 1st, 1915, he started having severe fits, and these continued up to his admission twenty-four hours later.
Some Observations on the Study of the Blood-pressure in the Insane
Authors: Parkin G. G. 
Published: August 2008

This paper is based upon observations taken on patients at rarkside Mental Hospital, Macclesfield.Martin's modification of a Riva-Rocci sphygmomanometer was used. The systolic pressure (S.P.) was taken at the point on the scale when the first audible click was heard through the stethoscope on decompression following obliteration of the left brachial artery, and the diastolic pressure (D.P.) at the point when the loud thuds suddenly became dull (the end of the third and beginning of the fourth phase).
Problems of Pyretotherapy in Paralytic Dementia
Authors: Eddison H. Wilfred 
Published: August 2008

Pyretotherapy, or the artificial induction of pyrexia as a means of treatment of the psychoses, has engaged the attention of psychiatrists for many years. The means employed to this end have been numerous, and they may be divided into two classes:1. Chemical: Hypodermic injections of sodium nucleinate; or of protein in the form of peptone, blood, milk, tuberculin or emulsions of dead bacilli.2. Infective: The introduction of living organisms, especially Plasmodium vivax malariæ and Spirochete recurrentis duuoni.
Terminal Uræmia: With Notes on the Prevalence of Renal Disease Amongst the Insane
Authors: Shera A. Geoffrey 
Published: August 2008

The high incidence of chronic interstitial nephritis at post-mortem examinations at the East Sussex County Mental Hospital prompted an investigation into the urea content of the cerebro-spinal fluid. In the years 1926-29, some 68% of all deaths have had post-mortem examinations performed, totalling over 200 autopsies, and a series of 60 successive results are tabulated below (Table I), giving the following details:
(1)The sex of the patient.(2)The age.(3)The interval between death and the estimation of the urea content of the cerebro-spinal fluid.(4)The result of the estimation.(5)The mental diagnosis.(6)Macroscopic evidence of gross renal disease (+ or −).(7)Other gross macroscopical abnormalities.
Faulty Detoxication in Schizophrenia
Authors: Quastel J. H. , Wales W. T. H. 
Published: August 2008

The hippuric acid excretion test (after benzoate administration) has been used by previous workers, with the general result that it affords a reasonably accurate and satisfactory test for determination of parenchymatous hepatic damage and of various hepatic involvements. The test is also known to be indicative of hepatic disorder, even where no clear clinical signs of hepatic or renal derangements are observable. A series of 67 cases of mental disorder has been examined by the test, 45 of which belonged to the schizophrenic group; 18 of these were classed as catatonics. The average value of hippuric acid eliminated in the non-catatonic schizophrenic group, expressed in terms of benzoic acid, in 4 hours after administration of 6 grm. of sodium benzoate, was 3.4 grm. with an average deviation from the mean of ± 0.4 grm. This value agrees well with the values obtained by previous workers for normal cases having no hepatic damage. The average value of hippuric acid eliminated under the same conditions by catatonic patients was 2.2 grm. with an average deviation from the mean of ± 0.5 grm. All the catatonic patients studied, without exception, showed a diminished ability to excrete hippuric acid at a normal rate. It is inferred that a metabolic disturbance of the liver affecting benzoic acid detoxication may be a characteristic feature of catatonic patients.Work on benzoic acid detoxication in catatonic patients before and after various shock treatments for schizophrenia is in progress.
Thrombo-Phlebitis Occurring in Patients Receiving Barbiturates
Authors: Palmer H. A. 
Published: August 2008

In the extensive literature on sleep therapy some fifty complications have been recorded by the various authors. In a previous article (Journ. Ment. Sci., November, 1937) these were listed (pp. 660, 661) and divided into four main groups as follows:
1.Common complications: Representing mainly normal by-products of the treatment.2.Complications involving particular tissues: Representing tissue idiosyncrasy.3.Accidents.4.True toxic complications: Representing a group which could not be regarded as either a necessary by-product of the treatment, an unavoidable expression of disproportionate sensitivity on the part of a particular tissue, or an accident which might be avoided.