bluuebunny/crossref_metadata_2025_split huggingface dataset:
4. On the Variations of the Fertility and Fecundity of Women according to Age
Authors: Duncan J. Matthews 
Published: June 2016

This paper was divided into four parts. In the first part it was shown :—1. That the actual, not the relative, fertility of our female population, as a whole, at different ages, increases from the commencement of the child-bearing period of life until the age of 30 is reached, and then declines to its extinction with the child-bearing faculty.2. That the actual fertility is much greater before the climax, 30 years, is reached, than after it is passed.
1. On Some Capillary Phenomena
Authors: Tait  
Published: June 2016

This communication was intended to illustrate by experiments with the solution of glycerine and oleate of soda, devised by Plateau, the mode in which a soap-bubble is detached as a closed shell from the mouth of a funnel; the mode in which two bubbles unite; and the process of cutting one into two or more.A statical investigation of the form of an unclosed film, blown with coal gas, was given (the kinetic problem presenting very grave difficulties), and the results were shown to be in accordance with observation, so far as the eye can follow the rapid change which takes place in the neck of the film just before the closed bubble is detached.
2. On Functions with Recurring Derivatives
Authors: Sang Edward 
Published: June 2016

In a previous paper, it was pointed out that the characteristic problem of the third branch of the higher calculus, is to discover the relation between the primary variable and its function, when the relation subsisting between the function and its derivative is known. The present paper treats of the solution of the simplest case of this general problem, that in which the function is equal or proportional to its derivative.The proposition in hand is naturally divided into cases, according to the order of derivation: The first two of these can, by well-known artifices, be brought under the dominion of the integral calculus, and their relations can therefore present nothing new. But for the sake of the continuity of the treatment, and of certain relationships which otherwise could not have been so well explained they have been discussed in the paper.
1. Some Observations on Incubation
Authors: Davy John 
Published: June 2016

In this paper its author describes the results of experiments made with two intents—one, to endeavour to ascertain whether there can be a complete arrest of vital action without the death of the egg; the other to ascertain the changes which take place in those instances in which, during incubation, the egg proves unproductive.The eggs used were chiefly those of the common fowl. The trials to which they were subjected were of three kinds—the airpump, the ice-house, and immersion in lime-water.
3. On tbe Operator φ(∇)
Authors: Tait  
Published: June 2016

AbstractBy combining, as above, Hamilton's linear and vector-function with his celebrated vector square-root of the negative of Laplace's operator, an operator of great use in physical applications of mathematics is obtained. With the notation employed in the author's paper “On Green's and other Allied Theorems,” Trans. R.S.E. 1870, § 17, it is shown to be generally expressible in the form ofwhere α,β,γ, are any three unit vectors (not necessarily rectangular), and α1,β1,γ1 any three vectors whatever.
7. On a Singular Case of Rectification in Lines of the Fourth Order
Authors: Sang Edward 
Published: June 2016

The class of curves resulting from the formulaare of considerable interest as occurring in various mechanical inquiries. When a straight wire, whose effective breadth and thickness are as two to one, is fixed at one end and made to vibrate, its free end describes a curve of which the general equation isin which k is constant for the particular variety of curve. When the curve becomes a parabola, and when k = 0, it takes the form above mentioned; these phases were exhibited by me in 1832. Again, when a system of toothed wheels is deduced from a straight rack, having a curve of sines for its outline, the points of contact describe a curve of this class, as is shown in my treatise on the teeth of wheels.
4. Additional Notes on the Occurrence of the Sperm-Whale in the Scottish Seas
Authors: Turner  
Published: June 2016

In a communication made to this Society on the 6th February, 1871, I noted the capture of a sperm-whale at Oban in May, 1829, and I collected from various sources records of the stranding of seven additional specimens on the Scottish coasts.Since that communication was published, a large sperm-whale has come ashore on the west coast of the Isle of Skye, some particulars concerning which I propose to relate in this communication.Tourists in Skye, during the past autumn, who visited Loch Corruisk by boat from Torrin, as they sailed up Loch Scavaig, became conscious, by another sense than that of sight, that a large animal in a state of putrefaction was in their immediate vicinity.
2. On the Carboniferous Volcanic Rocks in the Basin of the Firth of Forth—their Structure in the Field and under the Microscope
Authors: Geikie  
Published: June 2016

AbstractIn the introductory portion of the paper a sketch is given of the present state of opinion among Continental petrographers regarding volcanic rocks associated with palæozoic formations. The author points out that a relic of Werner's belief in the recentness of volcanic action may still be traced pervading the ideas of German geologists. In this paper he endeavours to show that, alike in their formation in the field and in their structure under the microscope, the basalts and tuffs of palæozoic time were as truly the products of volcanic action as the lavas and ashes of the present day.
4. On Comets
Authors: Tait  
Published: June 2016

AbstractThe author commenced by stating that he had been led to make farther investigations, on the subject of his hypothesis as to the nature of comets, by some comparatively recent criticism to which that hypothesis had been subjected. Its main features had been published more than ten years ago in the “Proceedings” of the Society (May 17, 1869) and in the first volume of “Nature.” Of course, if a critic completely misstates an hypothesis, he has no difficulty in refuting it; so that to such writers the author does not attempt to reply.
3. Mathematical Notes: (a.) On a Problem in Arrangements
Authors: Tait  
Published: June 2016

While making some algebraic problems last summer for an examination, I devised the following question:—“A schoolmaster went mad, and amused himself by arranging the boys. He turned the dux boy down one place, the new dux two places, the next three, and so on till every boy's place had been altered at least once. Then he began again, and so on; till, after 306 turnings down, all the boys got back to their original places. This disgusted him, and he kicked one boy out. Then he was amazed to find that he had to operate 1120 times before all got back to their original places. How many boys were in the class?”
4. Notice of the Completion of the new Rock Thermometers at the Royal Observatory, Edinburgh, and what they are for
Authors: Smyth Piazzi 
Published: June 2016

The nature of this paper may he understood from the following headings:—(1.) The making and placing of the new thermometers.(2.) Practically described by Mr Thomas Wedderburn.(3.) The problem with the old thermometers.(4.) Their next use in level fluctuations.(5.) Their employment by Sir Wm. Thomson.(6.) Their subsequent demonstration of the cycle of supra-annual waves of heat and cold.(7.) The published predictions in 1872 for 1878–80.(8.) The spoiled predictions in 1877, under the influence of erroneous sun-spot dates.(9.) The rectified predictions in 1879, when the true date of sunspot minimum was ascertained by direct observation.(10.) How to obtain correct dates for future sun-spot minima.
XVIII.—The Definite Integrals of Interpolation Theory
Authors: Copson E. T. 
Published: June 2016

It is well known that, if the infinite seriesis convergent for any non-integral value of z, it is uniformly convergent in any finite region of the z-plane and represents an integral function C(z), say, such that C(n) = an for n = 0, ± 1, ± 2, … It is called the Cardinal Function of the table of values, and is identical with Gauss's Interpolation Formula (suitably bracketed).The function C(z) defined by the series (1) has been given two different definite integral representations, due to Ferrar and Ogura respectively.
3. On the Figures of Equilibrium of Liquid Films
Authors: Brewster David 
Published: June 2016

In repeating some of the experiments of Professor Plateau, described in seven interesting memoirs published in “The Transactions of the Belgian Academy,” and in prosecuting his own experiments on the colours of the soap-bubble, the author of this paper observed several new phenomena which may have escaped the notice of the Belgian philosopher.Professor Plateau has described and drawn the beautiful systems of soap-films, obtained by lifting from a soap solution a cube made of wires about one and a half inch long. This system is a polyhedron, composed of twelve similar films stretching from the wires, and united to a plane quadrangular film in the centre. When this vertical film was blown upon, M. Von Rees observed that it was reduced to a line, and then reproduced in a horizontal position, from which it could be blown again into a vertical position.
4. Note on Professor Tait's “Quaternion Path” to Determinants of the Third Order
Authors: Martin Hugh 
Published: June 2016

I have read with much interest Professor Tait's “Note on Determinants of the Third Order” in the Proceedings of this Session (pp. 59–61), and admire the method of discovering new properties of Determinants. I am not sure, however, that the properties, when discovered, are more difficult of proof by Determinant methods, and I venture to submit the following as simple and elementary:—The first property, namely,is true under greater generality, and the Determinant proof is the same as for the special case.
7. On the Cell-Walls of Hepatic Cells
Authors: Haycraft John Berry 
Published: June 2016

Since Henle and Purkinje first described the cells which form the great mass of the liver, microscopists have maintained that these are what are termed “naked protoplasts”—that is, they possess, like the white blood corpuscle, no differentiated cell-walls. I may mention the names of Dr Lionel Beale, Ewald Hering (“Stricker's Histology,” section on the Liver), and Dr Klein (“Atlas of Histology”), who all agree in denying its existence. Indeed, the absence of this structure is emphatically insisted upon in most works on microscopical anatomy.If a liver-cell be examined with a power of about 300 diameters, it is seen to be a granular mass, of a somewhat spherical shape, containing a very distinct nucleus and nucleolus. The granules are but the optical expression of a delicate reticulum or stroma, which may be seen as such on using a higher power.
1. The Earthquake of 28th November 1880 in Scotland and Ireland
Authors: Stevenson Charles Alexander 
Published: June 2016

In 1877, my father, Mr David Stevenson, communicated to the Society a notice of earthquake shocks in Argyllshire (see Proceedings, vol. ix.) from observations made by the keepers at several lighthouses, which the late Dr Bryce undertook to use in his intended visit to the west of Scotland, to trace the source of the earthquake waves of 1877, an intention which, however, was suddenly terminated by his lamented accidental death at Inverness.Another earthquake shock, which visited Scotland and the north of Ireland on the 28th November 1880, has afforded the means of acquiring further observations, of which I think (in connection with those formerly given) the Society may consider it not unimportant to have a record in their Proceedings.
1. On the Colour of the Mediterranean and other Waters
Authors: Aitken John 
Published: June 2016

The investigation was at first undertaken with a view of determining how the blue colour of the water of the Mediterranean is produced, and of finding the explanation of the different colour phenomena seen in that sea. The investigation was afterwards extended to other waters.The experiments were made with a special view of determining whether the selective reflection or the selective absorption theory gave the correct explanation of the blueness seen in water.
On the Comparative Histology and Physiology of the Spleen
Authors: Whiting Arthur J. 
Published: June 2016

The principal subject of the author's research has been the comparative histology of the spleen in twenty-two different kinds of animals, embracing all the typical vertebrates from the fish to Man.The capsule of a typical mammalian spleen, such as that of the cat, consists of two layers, the outer composed of ordinary fibrous tissue, the inner of nonstriped muscle. The splenic artery and vein, as they enter the organ at the hilum, are enclosed in a sheath formed by an inflexion of the capsule, and, like it, consisting of a fibrous and a muscular layer, the fibrous layer being next the vessels, and the muscular layer external to it, adjoining the pulp.
Fazıl Say: A Turkish Musician in Europe
Authors: Durugönül Esma 
Published: June 2016

Identity isn’t given once and for all:it is built up and changes throughout a person’s lifetime.1The aim of this paper is to determine how and to what extent Fazıl Say, whose inspiration, according to his own words, is the bridge between Europe and Asia, has become an ambassador between Europe and Turkey.2 A further aim is to determine whether Fazıl Say may be referred to as ‘hybrid’ concerning both his person and his works. This will be done first by describing his background and then the conditions which led not only to his European, but also his global success. Assuming that not only his family, social environment and education were decisive in this process, the social changes that took place in Turkey following the foundation of the Turkish Republic in 1923 are detailed, with special consideration of the reforms directly affecting art and music. To offer more insight into this context, the mutual influences on music between the Ottoman Empire and Europe are outlined.
Prenatal programming: adverse cardiac programming by gestational testosterone excess
Authors: Vyas Arpita K. , Hoang Vanessa , Padmanabhan Vasantha , Gilbreath Ebony , Mietelka Kristy A. 
Published: June 2016

AbstractAdverse events during the prenatal and early postnatal period of life are associated with development of cardiovascular disease in adulthood. Prenatal exposure to excess testosterone (T) in sheep induces adverse reproductive and metabolic programming leading to polycystic ovarian syndrome, insulin resistance and hypertension in the female offspring. We hypothesized that prenatal T excess disrupts insulin signaling in the cardiac left ventricle leading to adverse cardiac programming. Left ventricular tissues were obtained from 2-year-old female sheep treated prenatally with T or oil (control) from days 30–90 of gestation. Molecular markers of insulin signaling and cardiac hypertrophy were analyzed. Prenatal T excess increased the gene expression of molecular markers involved in insulin signaling and those associated with cardiac hypertrophy and stress including insulin receptor substrate-1 (IRS-1), phosphatidyl inositol-3 kinase (PI3K), Mammalian target of rapamycin complex 1 (mTORC1), nuclear factor of activated T cells –c3 (NFATc3) and brain natriuretic peptide (BNP) compared to controls. Furthermore, prenatal T excess increased the phosphorylation of PI3K, AKT and mTOR. Myocardial disarray (multifocal) and increase in cardiomyocyte diameter was evident on histological investigation in T-treated females. These findings support adverse left ventricular remodeling by prenatal T excess.
Specification of jaw identity by the Hand2 transcription factor
Authors: Funato Noriko , Kokubo Hiroki , Nakamura Masataka , Yanagisawa Hiromi , Saga Yumiko 
Published: June 2016

AbstractAcquisition of the lower jaw (mandible) was evolutionarily important for jawed vertebrates. In humans, syndromic craniofacial malformations often accompany jaw anomalies. The basic helix-loop-helix transcription factor Hand2, which is conserved among jawed vertebrates, is expressed in the neural crest in the mandibular process but not in the maxillary process of the first branchial arch. Here, we provide evidence that Hand2 is sufficient for upper jaw (maxilla)-to-mandible transformation by regulating the expression of homeobox transcription factors in mice. Altered Hand2 expression in the neural crest transformed the maxillae into mandibles with duplicated Meckel’s cartilage, which resulted in an absence of the secondary palate. In Hand2-overexpressing mutants, non-Hox homeobox transcription factors were dysregulated. These results suggest that Hand2 regulates mandibular development through downstream genes of Hand2 and is therefore a major determinant of jaw identity. Hand2 may have influenced the evolutionary acquisition of the mandible and secondary palate.
AgIn: measuring the landscape of CpG methylation of individual repetitive elements
Authors: Suzuki Yuta , Korlach Jonas , Turner Stephen W. , Tsukahara Tatsuya , Taniguchi Junko , Qu Wei , Ichikawa Kazuki , Yoshimura Jun , Yurino Hideaki , Takahashi Yuji , Mitsui Jun , Ishiura Hiroyuki , Tsuji Shoji , Takeda Hiroyuki , Morishita Shinichi 
Published: June 2016

Abstract
Motivation: Determining the methylation state of regions with high copy numbers is challenging for second-generation sequencing, because the read length is insufficient to map reads uniquely, especially when repetitive regions are long and nearly identical to each other. Single-molecule real-time (SMRT) sequencing is a promising method for observing such regions, because it is not vulnerable to GC bias, it produces long read lengths, and its kinetic information is sensitive to DNA modifications.
Results: We propose a novel linear-time algorithm that combines the kinetic information for neighboring CpG sites and increases the confidence in identifying the methylation states of those sites. Using a practical read coverage of ∼30-fold from an inbred strain medaka (Oryzias latipes), we observed that both the sensitivity and precision of our method on individual CpG sites were ∼93.7%. We also observed a high correlation coefficient (R = 0.884) between our method and bisulfite sequencing, and for 92.0% of CpG sites, methylation levels ranging over [0,1] were in concordance within an acceptable difference 0.25. Using this method, we characterized the landscape of the methylation status of repetitive elements, such as LINEs, in the human genome, thereby revealing the strong correlation between CpG density and hypomethylation and detecting hypomethylation hot spots of LTRs and LINEs. We uncovered the methylation states for nearly identical active transposons, two novel LINE insertions of identity ∼99% and length 6050 base pairs (bp) in the human genome, and 16 Tol2 elements of identity &gt;99.8% and length 4682 bp in the medaka genome.
Availability and Implementation: AgIn (Aggregate on Intervals) is available at: https://github.com/hacone/AgIn
Contact: ysuzuki@cb.k.u-tokyo.ac.jp or moris@cb.k.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
STRUM: structure-based prediction of protein stability changes upon single-point mutation
Authors: Quan Lijun , Lv Qiang , Zhang Yang 
Published: June 2016

Abstract
Motivation: Mutations in human genome are mainly through single nucleotide polymorphism, some of which can affect stability and function of proteins, causing human diseases. Several methods have been proposed to predict the effect of mutations on protein stability; but most require features from experimental structure. Given the fast progress in protein structure prediction, this work explores the possibility to improve the mutation-induced stability change prediction using low-resolution structure modeling.
Results: We developed a new method (STRUM) for predicting stability change caused by single-point mutations. Starting from wild-type sequences, 3D models are constructed by the iterative threading assembly refinement (I-TASSER) simulations, where physics- and knowledge-based energy functions are derived on the I-TASSER models and used to train STRUM models through gradient boosting regression. STRUM was assessed by 5-fold cross validation on 3421 experimentally determined mutations from 150 proteins. The Pearson correlation coefficient (PCC) between predicted and measured changes of Gibbs free-energy gap, ΔΔG, upon mutation reaches 0.79 with a root-mean-square error 1.2 kcal/mol in the mutation-based cross-validations. The PCC reduces if separating training and test mutations from non-homologous proteins, which reflects inherent correlations in the current mutation sample. Nevertheless, the results significantly outperform other state-of-the-art methods, including those built on experimental protein structures. Detailed analyses show that the most sensitive features in STRUM are the physics-based energy terms on I-TASSER models and the conservation scores from multiple-threading template alignments. However, the ΔΔG prediction accuracy has only a marginal dependence on the accuracy of protein structure models as long as the global fold is correct. These data demonstrate the feasibility to use low-resolution structure modeling for high-accuracy stability change prediction upon point mutations.
Availability and Implementation: http://zhanglab.ccmb.med.umich.edu/STRUM/
Contact: qiang@suda.edu.cn and zhng@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The structural effects of mutations can aid in differential phenotype prediction of beta-myosin heavy chain (Myosin-7) missense variants
Authors: Al-Numair Nouf S. , Lopes Luis , Syrris Petros , Monserrat Lorenzo , Elliott Perry , Martin Andrew C. R. 
Published: June 2016

Abstract
Motivation: High-throughput sequencing platforms are increasingly used to screen patients with genetic disease for pathogenic mutations, but prediction of the effects of mutations remains challenging. Previously we developed SAAPdap (Single Amino Acid Polymorphism Data Analysis Pipeline) and SAAPpred (Single Amino Acid Polymorphism Predictor) that use a combination of rule-based structural measures to predict whether a missense genetic variant is pathogenic. Here we investigate whether the same methodology can be used to develop a differential phenotype predictor, which, once a mutation has been predicted as pathogenic, is able to distinguish between phenotypes—in this case the two major clinical phenotypes (hypertrophic cardiomyopathy, HCM and dilated cardiomyopathy, DCM) associated with mutations in the beta-myosin heavy chain (MYH7) gene product (Myosin-7).
Results: A random forest predictor trained on rule-based structural analyses together with structural clustering data gave a Matthews’ correlation coefficient (MCC) of 0.53 (accuracy, 75%). A post hoc removal of machine learning models that performed particularly badly, increased the performance (MCC = 0.61, Acc = 79%). This proof of concept suggests that methods used for pathogenicity prediction can be extended for use in differential phenotype prediction.
Availability and Implementation: Analyses were implemented in Perl and C and used the Java-based Weka machine learning environment. Please contact the authors for availability.
Contacts: andrew@bioinf.org.uk or andrew.martin@ucl.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.