bluuebunny/crossref_metadata_2025_split huggingface dataset:
Translating exome sequencing from research to clinical diagnostics
Authors: Coonrod Emily M. , Margraf Rebecca L. , Voelkerding Karl V. 
Published: August 2012

Abstract
In the relatively short time frame since the introduction of next generation sequencing, it has become a method of choice for complex genomic research studies. As a paradigm shifting technology, we are now witnessing its translation into clinical diagnostic laboratories for patient care. Multi-gene panels for a variety of disorders are now available in several clinical laboratories based on targeted gene enrichment followed by next generation sequencing. Genome wide interrogation of protein coding regions, or exome sequencing, has been successfully and increasingly applied in the research setting for the elucidation of candidate genes and causal variants in individuals and families with a diversity of rare and complex genetic disorders. Based on this progress, exome sequencing is also beginning a translational process into clinical practice. However, introducing exome sequencing as a diagnostic modality poses new technical and bioinformatics challenges for clinical laboratories. In this review, we present technical and bioinformatics aspects of exome sequencing, describe representative examples from the literature of how exome sequencing has been used for candidate gene discovery, and discuss considerations for its clinical translation.
IFCC standardised HbA1c: should the world be as one?
Authors: John Garry , English Emma 
Published: August 2012

Abstract
The central importance of HbA1c in monitoring glycaemic control was highlighted by the Diabetes Control and Complications Trial (DCCT) which showed that improved glycaemic control, as monitored by HbA1c, delayed the onset of diabetic complications. Following this publication the issue of international standardisation of glycated haemoglobin (GHb) measurements became an important objective. The lack of international standardisation resulted in several countries developing National Standardisation Programmes. The International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) Working Group on HbA1cStandardisation has established a reference measurement procedure (HPLC-MS or HPLC-CE) for HbA1c embracing the concept of metrological traceability. The reference method is anchored to a global network of 15 approved reference laboratories; this confers sustainability and a low level of uncertainty. Essential elements of a comprehensive reference measurement system additionally include the definition of the measurand and the unit of measurement. HbA1c is defined as haemoglobin (Hb) molecules having a stable adduct of glucose to the N-terminal valine of the β chain [Hb β chain (Blood) – N-(1-deoxyfructos-1-yl) Hb β chain] and that mmol/mol be used as the unit of measurement. These developments will result in improvements in inter-method and inter-laboratory agreement. Additionally, global acceptance of standardisation based on metrologically sound principles will enable clinical goals and diagnostic guidelines to be developed that can be adopted by all countries.
Suitability of POC lactate methods for fetal and perinatal lactate testing: considerations for accuracy, specificity and decision making criteria
Authors: Orsonneau Jean-Luc , Fraissinet François , Sébille-Rivain Véronique , Dudouet Daniele , Bigot-Corbel Edith 
Published: August 2012

Abstract

Background: Point of care (POC) testing for fetal scalp blood lactate is a more user friendly and more successful approach compared to scalp pH for intrapartum fetal monitoring. The aim of this study was to assess the analytical specificity and clinical reliability of three POC lactate methods.

Methods: The analytical performance of three POC lactate methods was compared to Cobas 6000 (Roche Diagnostics) laboratory reference method: Lactate Pro from Arkray, GEM 4000 from Instrumentation Laboratory and StatStrip Lactate from Nova Biomedical. The clinical performance and influences on accuracy and decision making criteria for the three POC methods was assessed with umbilical cord samples and compared to the laboratory reference method. The influence of varying ranges of hemoglobin, pH and partial oxygen pressure (pO2) on the accuracy of results was assessed.

Results: Although all three POC methods showed good correlation with the reference method for the umbilical cord sample population (r=0.989, 0.973 and 0.980, respectively), Lactate Pro and Gem 4000 showed a significant negative bias compared to the reference method. The degree of bias meant a significant readjustment of decision making criteria was required for fetal lactate use. The accuracy of the Lactate Pro results was affected by hemoglobin and to a lesser extent pH.

Conclusions: The three electrochemical POC devices can measure fetal lactate reliably. StatStrip Lactate showed a closer correlation and concordance to our laboratory reference method. The results of this study indicate the requirement for predetermining the reliability of POC lactate methods before use present in fetal and perinatal settings.
Applications of a transcendence criterion for reciprocal sums of binary linear recurrences
Authors: Kurosawa Takeshi 
Published: August 2012

Abstract
Let {R

n
}
n≥0 be a binary recurrence defined by
R

n+2 = A
R

n+1 + B
Rn
(n ≥ 0), where
A, B, R
0, R
1 are integers and
Δ = A
2 + 4B > 0 is not a perfect square.
We show a necessary and sufficient condition for the transcendency of the sum

∑

k
≥
0
,

R

r
k

≠
-

b
k

a
k

R

r
k

+

b
k

,

$
{\sum _{k\ge 0, {R_{r^k}\ne -b_k}}\frac{a_k}{R_{r^k}+b_k}},
$

where r ≥ 2 is an integer
and {a

k
}
k≥0 and {b

k
}
k≥0 are sequences of algebraic numbers satisfying
certain growth conditions. For the proof, we apply the transcendence criterion for Mahler type
functions of several variables which gives equivalence between the rationality of the function
and the algebraicity of its values at algebraic points.
Influence of hygromechanical history on the longitudinal mechanosorptive creep of wood
Authors: Montero Cédric , Gril Joseph , Legeas Clémentine , Hunt David G. , Clair Bruno 
Published: August 2012

Abstract
An experiment was performed on Norway spruce to simplify our understanding of mechanosorptive creep. Two well-matched sets of specimens were subjected to the same humidity history but loaded in four-point bending at different times. One set was loaded dry, and thus experienced a considerable creep at first adsorption (the so-called ++ effect). The other set was then loaded wet and only exhibited, together with the dry-loaded set, the usual pattern of creep increase during drying (- effect) followed by a partial recovery during remoistening (+ effect). Both sets converged to the same response after a few cycles. The results confirm that a single type of mechanosorption, combined with strain-dependent hygroexpansion and humidity-dependent viscoelascity, is sufficient to account for all observed features of longitudinal creep of wood at ambient temperature.
Distribution of extracts including 4,8-dihydroxy-5-methoxy-2-naphthaldehyde in Diospyros kaki analyzed by gas chromatography-mass spectrometry and time-of-flight secondary ion mass spectrometry
Authors: Matsushita Yasuyuki , Jang In-Cheol , Imai Takanori , Takama Ruka , Saito Kaori , Masumi Takashi , Lee Seung-Cheol , Fukushima Kazuhiko 
Published: August 2012

Abstract
The distribution of ethyl acetate extracts and 4,8-dihydroxy-5-methoxy-2-naphthaldehyde (compound I), which is a major constituent of the extracts obtained from the blackened heartwood of Diospyros kaki, was analyzed via gas chromatography-mass spectrometry (GC-MS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). According to GC-MS, the extracts and compound I are high in concentration at the pith and at the edges of the blackened heartwood. ToF-SIMS analysis revealed a peak at a mass-to-charge ratio of (m/z) 218, which is characteristic of the ionic form of compound I. The ToF-SIMS imaging of compound I in the blackened heartwood based on m/z 218 shows that compound I is located in parenchyma cells and their neighboring axial elements.
Testing of the superhydrophobicity of a zinc oxide nanorod array coating on wood surface prepared by hydrothermal treatment
Authors: Fu Yanchun , Yu Haipeng , Sun Qingfeng , Li Gang , Liu Yongzhuang 
Published: August 2012

Abstract
Natural wood surface is hydrophilic and can easily absorb moisture. Inorganic nanometer-scale metal oxides can be controlled and fabricated on wood surface to serve as a protective coating. In the present study, a superhydrophobic surface consisting of zinc oxide (ZnO) nanorod array was successfully attached on wood via a cosolvent hydrothermal method at low temperature. By means of X-ray diffraction pattern and Fourier transform infrared spectroscopy, the presence of the hexagonal wurtzite phase of ZnO was detected and characterized. Field-emission scanning electron microscopy showed uniform, large-scale rod-like ZnO crystal whiskers on the wood surface. The wettability of the wood surface after treatment became superhydrophobic, with a water contact angle of 153°. The prepared coating also showed an anti-contamination effect against milk, cola, soya sauces and coffee.
Functional characterization of the Mycobacterium tuberculosis zinc metallopeptidase Zmp1 and identification of potential substrates
Authors: Petrera Agnese , Amstutz Beat , Gioia Magda , Hähnlein Janine , Baici Antonio , Selchow Petra , Ferraris Davide M. , Rizzi Menico , Sbardella Diego , Marini Stefano , Coletta Massimo , Sander Peter 
Published: August 2012

Abstract
Zinc metallopeptidases of bacterial pathogens are widely distributed virulence factors and represent promising pharmacological targets. In this work, we have characterized Zmp1, a zinc metallopeptidase identified as a virulence factor of Mycobacterium tuberculosis and belonging to the neprilysin (NEP; M13) family, whose X-ray structure has been recently solved. Interestingly, this enzyme shows an optimum activity toward a fluorogenic substrate at moderately acidic pH values (i.e., 6.3), which corresponds to those reported for the Mtb phagosome where this enzyme should exert its pathological activity. Substrate specificity of Zmp1 was investigated by screening a peptide library. Several sequences derived from biologically relevant proteins were identified as possible substrates, including the neuropeptides bradykinin, neurotensin, and neuropeptide FF. Further, subsequences of other small bioactive peptides were found among most frequently cleaved sites, e.g., apelin-13 and substance P. We determined the specific cleavage site within neuropeptides by mass spectrometry, observing that hydrophobic amino acids, mainly phenylalanine and isoleucine, are overrepresented at position P1′. In addition, the enzymatic mechanism of Zmp1 toward these neuropeptides has been characterized, displaying some differences with respect to the synthetic fluorogenic substrate and indicating that the enzyme adapts its enzymatic action to different substrates.
Platelet function and thymosin β4
Authors: Kaur Harmanpreet , Mutus Bulent 
Published: August 2012

Abstract
Thymosin β4 (Tβ4) is a small, low-molecular-weight peptide ubiquitously expressed in all cells and extracellular fluids. It is a major actin sequestering protein present in the cells. In addition to this, Tβ4 has also been shown to be involved in endothelial cell migration, angiogenesis, corneal wound healing, and stem cell differentiation. It is also released by platelets after activation. The amount of Tβ4 increases at sites of injury and thus suggests an important role of this biopeptide in wound healing. Herein, we provide an overview of the role of Tβ4 in thrombosis and platelet aggregation.
A catalogue of putative HIV-1 protease host cell substrates
Authors: Impens Francis , Timmerman Evy , Staes An , Moens Kathleen , Ariën Kevin K. , Verhasselt Bruno , Vandekerckhove Joël , Gevaert Kris 
Published: August 2012

Abstract
Processing of human immunodeficiency virus (HIV) proteins by the HIV-1 protease is essential for HIV infectivity. In addition, several studies have revealed cleavage of human proteins by this viral protease during infection; however, no large-scale HIV-1 protease degradomics study has yet been performed. To identify putative host substrates in an unbiased manner and on a proteome-wide scale, we used positional proteomics to identify peptides reporting protein processing by the HIV-1 protease, and a catalogue of over 120 cellular HIV-1 protease substrates processed in vitro was generated. This catalogue includes previously reported substrates as well as recently described interaction partners of HIV-1 proteins. Cleavage site alignments revealed a specificity profile in good correlation with previous studies, even though the ELLE consensus motif was not cleaved efficiently when incorporated into peptide substrates due to subsite cooperativity. Our results are further discussed in the context of HIV-1 infection and the complex substrate recognition by the viral protease.
Disruption of gingipain oligomerization into non-covalent cell-surface attached complexes
Authors: Sztukowska Maryta , Veillard Florian , Potempa Barbara , Bogyo Matthew , Enghild Jan J. , Thogersen Ida B. , Nguyen Ky-Anh , Potempa Jan 
Published: August 2012

Abstract
RgpA and Kgp gingipains are non-covalent complexes of endoprotease catalytic and hemagglutinin-adhesin domains on the surface of Porphyromonas gingivalis. A motif conserved in each domain has been suggested to function as an oligomerization motif. We tested this hypothesis by mutating motif residues to hexahistidine or insertion of hexahistidine tag to disrupt the motif within the Kgp catalytic domain. All modifications led to the secretion of entire Kgp activity into the growth media, predominantly in a form without functional His-tag. This confirmed the role of the conserved motif in correct posttranslational proteolytic processing and assembly of the multidomain complexes.
Adipose triglyceride lipase in immune response, inflammation, and atherosclerosis
Authors: Radovic Branislav , Aflaki Elma , Kratky Dagmar 
Published: August 2012

Abstract
Consistent with its central importance in lipid and energy homeostasis, lipolysis occurs in essentially all tissues and cell types, including macrophages. The hydrolytic cleavage of triacylglycerol by adipose triglyceride lipase (ATGL) generates non-esterified fatty acids, which are subsequently used as essential precursors for lipid and membrane synthesis, mediators in cell signaling processes or as energy substrate in mitochondria. This review summarizes the current knowledge concerning the consequences of ATGL deficiency in macrophages with particular emphasis on macrophage (dys)-function, apoptosis, and atherosclerosis.
The analysis of N-glycans of cell membrane proteins from human hematopoietic cell lines reveals distinctions in their pattern
Authors: Reinke Stefan O. , Bayer Marion , Berger Markus , Hinderlich Stephan , Blanchard Véronique 
Published: August 2012

Abstract
Human cell lines are often different in their features and present variations in the glycosylation patterns of cell membrane proteins. Protein glycosylation is the most common posttranslational modification and plays a particular role in functionality and bioactivity. The key approach of this study is the comparative analysis of five hematopoietic cell lines for their N-glycosylation pattern. The N-glycans of membrane proteins were elucidated by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and MALDI-TOF/TOF-MS analyses. Furthermore, the expression of a set of glycosyltransferases was determined via RT-PCR. The B-lymphoma BJA-B and promyelocytic HL-60 cell lines distinguish in levels and linkages of glycan-bound sialic acids. Furthermore, subclones of BJA-B and HL-60 cells, which completely lack UDP-N-acetylglucosamine 2-ēpimerase/N-acetylmannosamine kinase (GNE), the key enzyme of sialic acid biosynthesis, contained almost no sialylated N-glycans. Compared to wild-type cells, the GNE-deficient cells pres\xadented a similar cell surface N-glycosylation pattern in terms of antennarity and fucosylation. The Jurkat T-cell line revealed only partially sialylated N-glycans. Additionally, the different hematopoietic cell lines vary in their level of bisecting GlcNAcylation and antennary fucosylation with the quantities of bisecting N-acetylglucosamine (GlcNAc) and core fucose coinciding with the expression of GnT-III and FucT-VIII. Of note is the occurrence of N-acetyllactosamine (LacNAc) extensions on tetraantennary structures in GNE-deficient cell lines.
Effect of tenofovir, an antiretroviral drug, on hepatic and renal functional indices of Wistar rats: protective role of vitamin E
Authors: Adaramoye Oluwatosin Adekunle , Adewumi Olubusuyi Moses , Adesanoye Omolola Abidemi , Faokunla Opeyemi Olubunmi , Farombi Ebenezer Olatunde 
Published: August 2012

Abstract

Background: Tenofovir (TFR) is a nucleotide reverse transcriptase inhibitor with activity against human immunodeficiency virus. We studied the effect of TFR administered to Wistar rats on hepatic and renal function markers and the possible modulatory role of vitamin E (Vit E).

Methods: The study consists of four groups of six rats each. The first group served as control, the second group received TFR at 50 mg/kg/day for 4 weeks, third group received TFR and Vit E, and the last group received Vit E alone.

Results: TFR administration caused a significant (p<0.05) increase in the levels of serum urea, creatinine, urinary glucose, and protein by 65%, 51%, 88%, and 79%, respectively, relative to controls. This was followed by a significant (p<0.05) reduction in creatinine clearance of TFR-treated rats. There were no significant differences (p>0.05) in the activities of serum aminotransferases, γ-glutamyltransferase, and alkaline phosphatase in TRF-treated rats relative to controls. TFR administration caused a marked elevation of malondialdehyde (MDA; index of lipid peroxidation) in the animals. Specifically, serum, hepatic, and renal MDA levels increased by 75%, 90%, and 102%, respectively. TRF-treated rats had significantly (p<0.05) reduced activities of renal catalase, glutathione-S-transferase, and superoxide dismutase. Supplementation of Vit E ameliorated TFR-induced effects by decreasing the levels of MDA and enhancing the activities of renal antioxidative enzymes. The biochemical data were supported by histopathological findings from the slides.

Conclusions: TFR increased oxidative stress and altered kidney function markers in the rats, whereas supplementation of Vit E attenuated these effects.
Correlation between an absence of cervical gland area on transvaginal sonography and cervical mucus hyaluronic acid levels in women with threatened preterm delivery
Authors: Tateyama Naoko , Asakura Hirobumi , Takeshita Toshiyuki 
Published: August 2012

Abstract

Purpose: Transvaginal sonographic findings of an absent cervical gland area (CGA) and a short cervical length (CL) are frequently observed in patients with threatened preterm delivery. The present study aimed to clarify whether sonographic findings are due to active production of hyaluronic acid (HA) in the cervix.

Methods: Possible relationships between sonographic findings of the presence or absence of the CGA and/or a short CL and cervical mucus HA concentration were investigated in 68 women with threatened preterm delivery at 22–31 weeks’ gestation and 136 women without threatened preterm delivery as controls.

Results: HA levels were higher in women with threatened preterm delivery (68.0 ng/mL) than in controls (39.0 ng/mL; P=0.001). Similarly, HA levels were higher in women with preterm labor showing an absent CGA and a short CL than in women with threatened preterm delivery without such findings (P<0.01). Stepwise multivariate logistic regression identified an absent CGA and threatened preterm delivery as independent predictors of high HA levels (P=0.04). HA concentration was not predictive for preterm delivery.

Conclusion: A sonographic finding of an absent CGA reflects high HA levels in the cervix with threatened preterm delivery.
Young’s modulus and prediction of plastics/elastomer blends
Authors: Liang Ji-Zhao , Ma Wen-Yong 
Published: August 2012

Abstract
The tensile stress and strain under small deformation for plastics/elastomer blends were analyzed, based on a geometric model and mechanical element model, and a Young’s modulus equation was derived based on the hypothesis with equal strain and Hooke’s law. The polypropylene (PP)/polyolefin elastomer (POE) blends were prepared by means of a twin screw extruder, and the Young’s modulus was measured at room temperature. It was found that the Young’s modulus decreased nonlinearly with increase in the POE volume fraction. The Young’s modulus of the PP/POE blends was estimated using the equation and was compared with the measured data. There was good agreement between them. Moreover, the Young’s modulus of PP/ethylene propylene diene monomer (EPDM) rubber EPDM blends at room temperature was estimated respectively using this equation and the mingling rule equation, as well as Liang’s equation published in the literature. The results showed that the calculations with this equation were closer to the experimental data reported in reference than those with the other two equations.
Green composites based on recycled polyamide-6/recycled polypropylene kenaf composites: mechanical, thermal and morphological properties
Authors: Sukri Suhailah Mohd , Suradi Nor Liyana , Arsad Agus , Rahmat Abdul Razak , Hassan Azman 
Published: August 2012

Abstract
The objective of this work was to investigate the effect of kenaf contents on mechanical, thermal and morphological properties of recycled polyamide-6 (rPA-6)/recycled polypropylene (rPP) blends. Kenaf was used to enhance the properties of composites. Alkali treating of kenaf by sodium hydroxide (NaOH) and combination with propylene grafted maleic anhydride (PPgMA) as a compatibilizer produced good adhesion both between rPP and rPA-6, and rPA-6/rPP and kenaf. Tensile, flexural and Izod impact tests were evaluated to study the mechanical properties. Differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) tests were carried out to investigate thermal properties. Scanning electron microscopy (SEM) was performed for morphological analysis. Generally, the mechanical properties were successfully enhanced, especially Young’s modulus, flexural modulus, flexural strength and elongation at break, while there were some problems which caused the tensile strength and impact strength to be inferior. Thermal analysis showed that the crystallization of composites decreased as kenaf contents were increased. SEM showed a problem with kenaf and rPP/rPA-6 compatibility, which led to insufficient matrix at some places and agglomeration of kenaf at other places. Morphologically, there was unidirectional presence of kenaf in rPP main composites and random orientation in rPA-6 main composites.