bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect size, confidence interval and statistical significance: a practical guide for biologists
Authors: Nakagawa Shinichi , Cuthill Innes C. 
Published: October 2007

AbstractNull hypothesis significance testing (NHST) is the dominant statistical approach in biology, although it has many, frequently unappreciated, problems. Most importantly, NHST does not provide us with two crucial pieces of information: (1) the magnitude of an effect of interest, and (2) the precision of the estimate of the magnitude of that effect. All biologists should be ultimately interested in biological importance, which may be assessed using the magnitude of an effect, but not its statistical significance. Therefore, we advocate presentation of measures of the magnitude of effects (i.e. effect size statistics) and their confidence intervals (CIs) in all biological journals. Combined use of an effect size and its CIs enables one to assess the relationships within data more effectively than the use ofpvalues, regardless of statistical significance. In addition, routine presentation of effect sizes will encourage researchers to view their results in the context of previous research and facilitate the incorporation of results into future meta‐analysis, which has been increasingly used as the standard method of quantitative review in biology. In this article, we extensively discuss two dimensionless (and thus standardised) classes of effect size statistics:dstatistics (standardised mean difference) andrstatistics (correlation coefficient), because these can be calculated from almost all study designs and also because their calculations are essential for meta‐analysis. However, our focus on these standardised effect size statistics does not mean unstandardised effect size statistics (e.g. mean difference and regression coefficient) are less important. We provide potential solutions for four main technical problems researchers may encounter when calculating effect size and CIs: (1) when covariates exist, (2) when bias in estimating effect size is possible, (3) when data have non‐normal error structure and/or variances, and (4) when data are non‐independent. Although interpretations of effect sizes are often difficult, we provide some pointers to help researchers. This paper serves both as a beginner’s instruction manual and a stimulus for changing statistical practice for the better in the biological sciences.
Morphologic changes associated with functional adaptation of the navicular bone of horses
Authors: Bentley V. A. , Sample S. J. , Livesey M. A. , Scollay M. C. , Radtke C. L. , Frank J. D. , Kalscheur V. L. , Muir P. 
Published: October 2007

AbstractFailure of functional adaptation to protect the skeleton from damage is common and is often associated with targeted remodeling of bone microdamage. Horses provide a suitable model for studying loading‐related skeletal disease because horses are physically active, their exercise is usually regulated, and adaptive failure of various skeletal sites is common. We performed a histologic study of the navicular bone of three groups of horses: (1) young racing Thoroughbreds (n = 10); (2) young unshod ponies (n = 10); and (3) older horses with navicular syndrome (n = 6). Navicular syndrome is a painful condition that is a common cause of lameness and is associated with extensive remodeling of the navicular bone; a sesamoid bone located within the hoof which articulates with the second and third phalanges dorsally. The following variables were quantified: volumetric bone mineral density; cortical thickness (Ct.Th); bone volume fraction, microcrack surface density; density of osteocytes and empty lacunae; and resorption space density. Birefringence of bone collagen was also determined using circularly polarized light microscopy and disruption of the lacunocanalicular network was examined using confocal microscopy. Remodeling of the navicular bone resulted in formation of transverse secondary osteons orientated in a lateral to medial direction; bone collagen was similarly orientated. In horses with navicular syndrome, remodeling often led to the formation of intracortical cysts and development of multiple tidemarks at the articular surface. These changes were associated with high microcrack surface density, low bone volume fraction, low density of osteocytes, and poor osteocyte connectivity. Empty lacunae were increased in Thoroughbreds. Resorption space density was not increased in horses with navicular syndrome. Taken together, these data suggest that the navicular bone may experience habitual bending across the sagittal plane. Consequences of cumulative cyclic loading in horses with navicular syndrome include arthritic degeneration of adjacent joints and adaptive failure of the navicular bone, with accumulation of microdamage and associated low bone mass, poor osteocyte connectivity, and low osteocyte density, but not formation of greater numbers of resorption spaces.
Age estimation in the Mediterranean bottlenose dolphinTursiops truncatus(Montagu 1821) by bone density of the thoracic limb
Authors: Butti Camilla , Corain Livio , Cozzi Bruno , Podestà Michela , Pirone Andrea , Affronte Marco , Zotti Alessandro 
Published: October 2007

AbstractThe determination of age is an important step in defining the life history traits of individuals and populations. Age determination of odontocetes is mainly based on counting annual growth layer groups in the teeth. However, this useful method is always invasive, requiring the cutting of at least one tooth, and sometimes the results are difficult to interpret. Based on the concept that bone matrix is constantly deposited throughout life, we analysed the bone mineral density of the arm and forearm of a series of bottlenose dolphins (Tursiops truncatus, Montagu 1821) stranded along the Italian coast of the Adriatic Sea or maintained in confined waters. The bone mineral density values we obtained were evaluated as possible age predictors of the Mediterranean population of this species, considering age as determined by counting growth layer groups in sections of the teeth and the total body length of the animal as references. Comparisons between left and right flipper showed no difference. Our results show that bone mineral density values of the thoracic limb are indeed reliable age predictors inTursiops truncatus. Further investigations in additional odontocete species are necessary to provide strong evidence of the reliability of bone mineral density as an indicator of growth and chronological wear and tear in toothed‐whales.
Initial motor axon outgrowth from the developing central nervous system
Authors: Fraher J. P. , Dockery P. , O'Donoghue O. , Riedewald B. , O’Leary D. 
Published: October 2007

AbstractRat and chick studies show that the earliest motor rootlet axon bundles emerge from all levels of the neural tube between radial glial end feet which comprise the presumptive glia limitans. The loose arrangement of the end feet at the time of emergence facilitates this passage. The points of emergence are regularly spaced in relation to the long axis of the neural tube and are not defined by any cell contact with its surface. Each rootlet carries a covering of basal lamina from the neural tube surface, which forms a sleeve around it. It is only after bundles of ventral rootlet axons have emerged that cells associate with them, forming clusters on the rootlet surface at a distance peripheral to the CNS surface of both species. A tight collar of glial end feet develops around the axon bundle at the neural tube surface shortly after initial emergence. These arrangements are in sharp contrast to those seen in the sensory rootlets, where clusters of boundary cap cells prefigure the sensory entry zones at the attachments of the prospective dorsal spinal and cranial sensory rootlets. Boundary cap cells resemble cluster cells and a neural crest origin seems the most likely for them. The study clearly demonstrates that no features resembling boundary caps are found in relation to the developing motor exit points.
Immunohistochemical analysis of Sonic hedgehog signalling in normal human urinary tract development
Authors: Jenkins Dagan , Winyard Paul J. D. , Woolf Adrian S. 
Published: October 2007

AbstractStudies of mouse mutants have demonstrated that Sonic hedgehog (SHH) signalling has a functional role in morphogenesis and differentiation at multiple sites within the forming urinary tract, and urinary tract malformations have been reported in humans with mutations that disrupt SHH signalling. However, there is only strikingly sparse and fragmentary information about the expression of SHH and associated signalling genes in normal human urinary tract development. We used immunohistochemistry to demonstrate that SHH protein was localised in distinct urinary tract epithelia in developing normal humans, in the urothelium of the nascent bladder and in kidney medullary collecting ducts. The expression patterns of the SHH‐transducing proteins Patched (PTCH) and Smoothened (SMO) were consistent with long‐range paracrine signalling associated with detrusor smooth muscle differentiation in the urogenital sinus. In the developing kidney, SHH and PTCH were expressed in epithelia of the collecting system between 16–26 weeks – surprisingly, SMO was not detected. Analysis of cell proliferation and Cyclin B1 immunohistochemistry at 26 weeks, as compared with a 28 week sample in which SHH expression was down‐regulated, was consistent with the idea that SHH and PTCH might influence medullary collecting duct growth by regulating the subcellular localisation of Cyclin B1 independently of SMO. Collectively, these descriptive results generate new hypotheses regarding SHH signal transduction in human urinary tract development and help to explain the varied urinary tract malformation phenotypes noted in individuals with mutations in the SHH pathway.
Influence of gelatin and starch on the instrumental and sensory texture of stirred yogurt
Authors: ARES GASTÓN , GONÇALVEZ DENISSE , PÉREZ CECILIA , REOLÓN GABRIELA , SEGURA NADIA , LEMA PATRICIA , GÁMBARO ADRIANA 
Published: October 2007

The effect of the addition of gelatin and starch on the rheological and sensory texture properties of sweetened plain stirred yogurt was studied. Six samples were prepared: two with gelatin (3 and 6 mg/g), three with starch (1, 5 and 10 mg/g) and a control sample without thickener. Rheological measurements were performed and flow curves were modelled according to the Herschel–Bulkley rheological model. Also, sensory evaluation was carried out using a trained panel. The addition of gelatin and starch significantly affected the instrumental texture parameters (Herschel–Bulkley's model parameters and syneresis) and the perceived sensory texture of yogurts. All sensory descriptors were well predicted by the partial least squares regression of the instrumental parameters. The addition of thickeners significantly reduced syneresis. Samples produced with 6 mg/g of gelatin did not show syneresis and showed the highest sensory viscosity, creaminess and mouth‐feel. Therefore, the use of 6 mg/g of gelatin could be a reasonable concentration to use in the production of low‐fat yogurts.
Using near infrared spectroscopy for the determination of total solids and protein content in cheese curd
Authors: SULTANEH ALI , ROHM HARALD 
Published: October 2007

In‐line or on‐line monitoring requires fast and reliable methods for determining composition or processing variables. A near infrared spectroscopic method for the determination of solids and protein content in cheese curd has been developed. Based on approximately 250 curd samples, calibration models were built using partial least squares regression. The calibration models resulted in coefficients of determination of R2 = 0.994 for total solids and R2 = 0.985 for protein content for unhomogenized curd, which improved only slightly after subjecting the curd to homogenization. As confirmed by results that were obtained from a validation set, this suggests that near infrared spectroscopy is a potential and powerful method for the rapid monitoring of curd composition.
Functional properties of native and cheese whey protein concentrate powders
Authors: HEINO ANTTI T , UUSI‐RAUVA JANNE O , RANTAMÄKI PIRJO R , TOSSAVAINEN OLLI 
Published: October 2007

The objective of this study was to compare microfiltered native whey protein concentrate and traditional cheese whey protein concentrate powders and their functional properties. Solubility, viscosity, gelation, foaming properties, emulsification and water‐holding capacity were studied. The effect of spray and freeze drying methods on functional properties was evaluated. Gel strength varied from 0.11 to 0.65 N. Foaming stability and overrun varied from 0 to 29.3 min and from 230 to 2200%, respectively. Foaming and gelation properties were clearly better with native whey protein powders. Differences between drying methods were not observed but higher heat load decreased solubility.
Evaluation of de‐lipidated egg yolk and yeast autolysate as growth supplements for lactic acid bacteria culture
Authors: DJEGHRI‐HOCINE BAIDA , BOUKHEMIS MESSAOUDA , ZIDOUNE MOHAMMED NASREDDINE , AMRANE ABDELTIF 
Published: October 2007

Four strains of lactic acid bacteria (LAB) were cultivated on deproteinated whey supplemented with yeast autolysate (YA) and/or de‐lipidated egg yolk (DEY). Growth was compared to that recorded on the widely used MRS medium. The feasibility of the use of YA in place of yeast extract was confirmed. In the presence of YA in the medium, cell numeration gained nearly 1 log for only 0.4% DEY added in the culture medium, namely 0.1 g/L additional nitrogen, showing that DEY also supplies LAB growth in trace elements and growth factors like vitamins. If compared to the MRS medium, final cell numerations were about 1 log lower on deproteinated whey supplemented with YA and DEY, while the protein nitrogen ratio of both media was 2.7, showing the high potential of the tested supplements, and especially DEY. Subsequent works with higher and hydrolysed DEY may be therefore useful.
REST is a key regulator in brain‐specific homeobox gene expression during neuronal differentiation
Authors: Park So Yun , Kim Jae Bum , Han Yong‐Mahn 
Published: October 2007

AbstractBrain‐specific homeobox (Bsx) is specifically expressed at the early embryonic stages during brain development. Several studies show that Bsx plays important roles in brain development; however, the mechanisms of its transcriptional regulation remain to be established. In this study, we show that binding of repressor element silencing transcription factor (REST) to the neuron restrictive silencer element (NRSE) represses Bsx transcription in non‐neuronal P19 cells. The Bsx promoter contains several putative binding sites for transcription factors, including NRSE for REST and the GC box for the transcriptional activator, Sp1. Upon neuronal differentiation of P19 cells with retinoic acid, Bsx gene expression increased, whereas that of the REST gene decreased. Electrophoretic mobility shift analyses demonstrated that recombinant REST proteins bound the NRSE region of the Bsx promoter. In neuronal NS20Y cells, transcriptional activity of the Bsx promoter was decreased upon expression of REST. Moreover, dominant‐negative REST derepressed Bsx transcription in P19 cells. Sp1‐mediated transcriptional activity of the Bsx promoter was attenuated by treatment with mithramycin A, a GC box‐binding drug, but was enhanced upon mutation of NRSE. Co‐immunoprecipitation and chromatin immunoprecipitation assays showed that the Bsx promoter appeared to be modulated by direct interactions between REST and Sp1. The CpG sites of NRSE and GC box were completely unmethylated, signifying no interference of DNA methylation. Our results suggest that binding of REST to NRSE suppresses the Sp1‐mediated activation of Bsx in non‐neuronal cells.
Neural precursors derived from human embryonic stem cells maintain long‐term proliferation without losing the potential to differentiate into all three neural lineages, including dopaminergic neurons
Authors: Hong Sunghoi , Kang Un Jung , Isacson Ole , Kim Kwang‐Soo 
Published: October 2007

AbstractHuman embryonic stem (hES) cells have the ability to renew themselves and differentiate into multiple cell types upon exposure to appropriate signals. In particular, the ability of hES cells to differentiate into defined neural lineages, such as neurons, astrocytes, and oligodendrocytes, is fundamental to developing cell‐based therapies for neurodegenerative disorders and studying developmental mechanisms. However, the utilization of hES cells for basic and applied research is hampered by the lack of well‐defined methods to maintain their self‐renewal and direct their differentiation. Recently we reported that neural precursor (NP) cells derived from mouse ES cells maintained their potential to differentiate into dopaminergic (DA) neurons after significant expansion in vitro. We hypothesized that NP cells derived from hES cells (hES‐NP) could also undergo the same in vitro expansion and differentiation. To test this hypothesis, we passaged hES‐NP cells and analyzed their proliferative and developmental properties. We found that hES‐NP cells can proliferate approximately 380 000‐fold after in vitro expansion for 12 weeks and maintain their potential to generate Tuj1+ neurons, GFAP+ astrocytes, and O4+ oligodendrocytes as well as tyrosine hydroxylase‐positive (TH+) DA neurons. Furthermore, TH+ neurons originating from hES‐NP cells expressed other midbrain DA markers, including Nurr1, Pitx3, Engrail‐1, and aromatic l‐amino acid decarboxylase, and released significant amounts of DA. In addition, hES‐NP cells maintained their developmental potential through long‐term storage (over 2 years) in liquid nitrogen and multiple freeze–thaw cycles. These results demonstrate that hES‐NP cells have the ability to provide an expandable and unlimited human cell source that can develop into specific neuronal and glial subtypes.
Role of KATP channels in protection against neuronal excitatory insults
Authors: Soundarapandian Mangala M. , Zhong Xiaofen , Peng Lisheng , Wu Di , Lu Youming 
Published: October 2007

AbstractATP‐sensitive K+ (KATP) channels that are gated by intracellular ATP/ADP concentrations are a unique subtype of potassium channels and play an essential role in coupling intracellular metabolic events to electrical activity. Opening of KATP channels during energy deficits in the CNS induces efflux of potassium ions and in turn hyperpolarizes neurons. Thus, activation of KATP channels is thought to be able to counteract excitatory insults and protect against neuronal death. In this review, we bring together recent studies about what kinds of molecules are needed to build and regulate arrays of KATP channel functions in the CNS neurons. We propose a model to explain how KATP channel activation regulates glutamate release from the pre‐synaptic terminals and how this regulation protects against ischemic neuronal injury and epilepsy.
Intracellular accumulation of a mild‐denatured monomer of the human PrP fragment 90–231, as possible mechanism of its neurotoxic effects
Authors: Chiovitti Katia , Corsaro Alessandro , Thellung Stefano , Villa Valentina , Paludi Domenico , D’Arrigo Cristina , Russo Claudio , Perico Angelo , Ianieri Adriana , Di Cola Domenico , Vergara Alberto , Aceto Antonio , Florio Tullio 
Published: October 2007

AbstractBecause of high tendency of the prion protein (PrP) to aggregate, the exact PrP isoform responsible for prion diseases as well as the pathological mechanism that it activates remains still controversial. In this study, we show that a pre‐fibrillar, monomeric or small oligomeric conformation of the human PrP fragment 90–231 (hPrP90–231), rather than soluble or fibrillar large aggregates, represents the neurotoxic species. In particular, we demonstrate that monomeric mild‐denatured hPrP90–231 (incubated for 1 h at 53°C) induces SH‐SY5Y neuroblastoma cell death, while, when structured in large aggregates, it is ineffective. Using spectroscopic and cellular techniques we demonstrate that this toxic conformer is characterized by a high exposure of hydrophobic regions that favors the intracellular accumulation of the protein. Inside the cells hPrP90–231 is mainly compartmentalized into the lysosomes where it may trigger pro‐apoptotic ‘cell death’ signals. The PrP toxic conformation, which we have obtained inducing a controlled in vitro conformational change of the protein, might mimic mild‐unfolding events occurring in vivo, in the presence of specific mutations, oxidative reactions or proteolysis. Thus, in light of this model, we propose that novel therapeutic strategies, designed to inhibit the interaction of the toxic PrP with the plasmamembrane, could be beneficial to prevent the formation of intracellular neurotoxic aggregates and ultimately the neuronal death.
Mechanisms of [3H]glycine release from mouse spinal cord synaptosomes selectively labeled through GLYT2 transporters
Authors: Luccini Elisa , Raiteri Luca 
Published: October 2007

AbstractGlycine release has been rarely studied. The aim of this work was to characterize the release of the amino acid from spinal cord glycinergic nerve endings selectively pre‐labeled through glycine transporters of the GLYT2 type. Purified mouse spinal cord synaptosomes were incubated with [3H]glycine in the presence of the GLYT1 blocker N‐[(3R)‐3‐([1,1′‐biphenyl]‐4‐yloxy)‐3‐(4‐fluorophenyl)propyl]‐N‐methylglycine hydrochloride and exposed in superfusion to varying concentrations of KCl, 4‐aminopyridine (4‐AP), or veratridine. KCl (≤ 15 mmol/L), 4‐AP (up to 1 mmol/L), and veratridine (≤ 0.3 μmol/L)‐provoked [3H]glycine release by external Ca2+‐dependent, botulinum toxin C1‐sensitive, exocytosis. The overflows evoked by higher concentrations of K+ or veratridine involved external Ca2+‐independent mechanisms of different nature. Only the overflow evoked by 3 or 10 μmol/L veratridine occurred totally (3 μmol/L) or in part (10 μmol/L) by transporter reversal, being sensitive to the GLYT2 blockers 4‐benzyloxy‐3,5‐dimethoxy‐N‐[1‐(dimethylaminociclopentyl)‐methyl] benzamide or O‐[(2‐benzyloxyphenyl‐3‐flurophenyl)methyl]‐l‐serine; in contrast, the external Ca2+‐independent [3H]glycine overflow provoked by 50 mmol/L K+ was transporter‐independent. This component of K+‐evoked overflow and the GLYT2‐independent portion of the 10 μmol/L veratridine‐evoked overflow, were largely sensitive to the vesicle depletor bafilomycin or BAPTA‐AM and were prevented by blocking the mitochondrial Na+/Ca2+ exchanger with 7‐chloro‐5‐(2‐chlorophenyl)‐1,5‐dihydro‐4,1‐benzothiazepin‐2(3H)‐one, indicating the involvement of exocytosis triggered by intraterminal mitochondrial Ca2+ ions.