Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative proteomic analysis of human placenta derived from assisted reproductive technology

The aim of this study was to use proteomics‐based approach to examine differences in protein expression in placenta derived from assisted reproductive technology (ART) and normal pregnancy. Using 2‐DE we found that, compared with the control group, 12 spots in standard in vitro fertilization group and 18 spots in intracytoplasmic sperm injection group were identified as significantly differentially expressed proteins. Among them, six spots were differentially expressed in both standard IVF and ICSI groups with the same change tendency. Totally, 20 proteins were successfully identified by MALDI TOF/TOF MS, including proteins involved in the membrane traffic, metabolism, nucleic acid processing, stress response and cytoskeleton. Notably, five proteins detected to be differentially expressed in both ART groups were identified as annexin A3, hnRNP C1/C2, α‐SNAP, FTL and ATP5A. Some of the proteins were confirmed by Western blot and immunohistochemistry analysis. Our study allowed for the initial identification of these proteins related to various functions in placentation with significantly altered abundance in ART groups. The present results reveal that abnormal protein profiles are involved in ART placenta and these differentially expressed proteins may be valuable for the evaluation of potential association between ART treatment and offspring outcome.
Two- and three-dimensional assembled structures constructed from amidate-bridged paddlewheel complexes with group 6 oxometallate ions.

Monocationic acetamidate-bridged dinuclear units are two-dimensionally connected by axially coordinating group 6 oxometallate ions in the structures [{M2(acam)4}2(M'O4)] (M = Rh, Ru; M' = Cr, Mo, W; Hacam = acetamide). In these sheet structures, dinuclear units are connected to each other by NH.O hydrogen bonds. The sheets are also connected with NH.O hydrogen bonds. Amidate-bridged dirhodium units that have bulkier alkyl groups reacted with CrO4(2-) or MoO4(2-) give three-dimensional diamondoid structures [{Rh2(pram)4}2(CrO4)] · 1.08H2O, [{Rh2(pram)4}2(MoO4)] · 2.44H2O and [{Rh2(buam)4}2(MoO4)] (Hpram = propionamide; Hbuam = butyramide). In these structures the NH group of the amidate ligands hydrogen bonds with O atoms in metallate ions.
Lipid Levels and Associated Cardiovascular Risk Factors in Moroccan Type 2 Diabetes: A Case Control Study (EPIDIAM Study)

Background : The management of diabetic dyslipidaemia, a well-recognized and modifiable risk factor, is a key element in the multifactorial approach to prevent cardiovascular diseases (CVD) in individuals with type 2 diabetes (T2DM). Objective : The aim of this study is to describe lipids profile and to compare CVD risk factors in Moroccan individuals with and without T2DM. Subjects and Methods : The study population consisted of 1307 unrelated T2D and 984 non-diabetics subjects. This was a case control study carried out in urban and rural primary health care centers. The survey was conducted from January 2006 to July 2008. Results : This case control study performed in a group of type 2 diabetic patients (1307) and non-diabetic (984) adults’ shows that T2D is strongly and independently associated with CVD risk factors, which are, hypertension (OR 4.06, 95% CI: 3.35-4.93, p <0.001), elevated TGs (OR 1.77, CI: 1.45-2.18, p <0.001), central obesity (OR 1.67, CI: 1.30-2.16, p <0.001), been female (OR 0.79, CI: 0.64-0.97, p =0.022), and been older-age (p =0.001). Strong prevalence of CVD risk factors has also shown among non-diabetics. Conclusion : The present study has found a high prevalence of CVD risk factors among T2D patients and controls despite the significant difference between them.
Proteome analysis of adipocyte lipid rafts reveals that gC1qR plays essential roles in adipogenesis and insulin signal transduction

Since insulin receptors and their downstream signaling molecules are organized in lipid rafts, proteomic analysis of adipocyte lipid rafts may provide new insights into the function of lipid rafts in adipogenesis and insulin signaling. To search for proteins involved in adipocyte differentiation and insulin signaling, we analyzed detergent‐resistant lipid raft proteins from 3T3‐L1 preadipocytes and adipocytes by 2‐DE. Eleven raft proteins were identified from adipocytes. One of the adipocyte‐specific proteins was globular C1q receptor (gC1qR), an acidic 32 kDa protein known as the receptor for the globular domain of complement C1q. The targeting of gC1qR into lipid rafts was significantly increased during adipogenesis, as determined by immunoblotting and immunofluorescence. Since the silencing of gC1qR by small RNA interference abolished adipogenesis and blocked insulin‐induced activation of insulin receptor, insulin receptor substrate‐1 (IRS‐1), Akt, and Erk1/2, we can conclude that gC1qR is an essential molecule involved in adipogenesis and insulin signaling.
Proteomics‐based identification of two novel direct targets of hypoxia‐inducible factor‐1 and their potential roles in migration/invasion of cancer cells

Hypoxia‐inducible factor‐1 (HIF‐1), consisting of oxygen‐sensitive HIF‐1α and constitutively expressed HIF‐1β subunits, is a master transcriptional activator for cellular response to hypoxia. To explore direct HIF‐1 targets, here we used differential gel electrophoresis (DIGE) to compare the HIF‐1‐regulated proteins between leukemic U937T‐cell line with and without conditional induction of HIF‐1α protein by tetracycline‐off system. Among the upregulated proteins identified, mRNA levels of annexin A1, macrophage‐capping protein (CapG), S100 calcium‐binding protein A4 (S100A4), S100A11, acyl‐CoA‐binding protein and calcyclin‐binding protein also increased. The expressions of the annexin A1, CapG and S100A4 genes were significantly induced by hypoxia in five adherent cell lines tested besides U937 cells, while their expressions were blocked by the short hairpin RNA specifically against HIF‐1α. Further luciferase reporter assay and chromatin immunoprecipitation showed that HIF‐1α directly bound to three hypoxia‐responsive elements located at intron 1 of S100A4 gene and hypoxia‐responsive element at −350 to −346 of CapG gene, which are essential for HIF‐1‐induced expression. Additionally, the role of S100A4 expression in migration and invasion of cancer cells were also confirmed. These findings would provide new sights for understanding the molecular mechanisms underlying HIF‐1 action.
Diurnal Variation in Coronary Flow Velocity Reserve in Healthy Men

Background. A number of cardiovascular diseases show diurnal variation. However, it is unknown whether coronary circulation exhibits diurnal variation.Methods. The flow velocities in the left anterior descending coronary artery of 15 healthy men were measured by transthoracic Doppler echocardiography both at rest and during intravenous infusion of adenosine triphosphate at 7 AM, noon, 5 PM and 9 PM. Coronary flow velocity reserve (CFVR) was calculated as the ratio of hyperemic to basal mean diastolic flow velocity. CFVR at 7 AM was significantly smaller than that at 9 PM (p=0.001; 7 AM, 3.23 ± 0.66; noon, 3.89 ± 0.86; 5 AM, 3.46 ± 0.65; 9 PM, 4.41 ± 1.11, respectively). CFVR at 5 PM was also significantly smaller than that at 9 PM (p=0.008). Conclusions. Diurnal variation in CFVR exists in healthy men. This finding may be related to the diurnal variation in cardiovascular events.
Comparative proteome and transcriptome analyses of embryonic stem cells during embryoid body‐based differentiation

Gene expression analyses of embryonic stem cells (ESCs) will help to uncover or further define signaling pathways and molecular mechanisms involved in the maintenance of self‐renewal and pluripotency. We employed a 2‐DE‐based proteomics approach to analyze human ESC line, Royan H5, in undifferentiated cells and different stages of spontaneous differentiation (days 3, 6, 12, and 20) by embryoid body formation. Out of 945 proteins reproducibly detected on gels, the expression of 96 spots changed during differentiation. Using MS, 87 ESC‐associated proteins were identified including several proteins involved in cell proliferation, cell apoptosis, transcription, translation, mRNA processing, and protein folding. Transcriptional changes accompanying differentiation of Royan H5 were also analyzed using microarrays. We developed a comprehensive data set that shows the use of human ESC lines in vitro to mimic gastrulation and organogenesis. Our results showed that proteomics and transcriptomics data are complementary rather than duplicative. Although regulation of many genes during differentiation were observed only at transcript level, modulation of several proteins was revealed only by proteome analysis.
Unintended changes in protein expression revealed by proteomic analysis of seeds from transgenic pea expressing a bean α‐amylase inhibitor gene

Seeds of genetically modified (GM) peas (Pisum sativum L.) expressing the gene for α‐amylase inhibitor‐1 (αAI1) from the common bean (Phaseolus vulgaris L. cv. Tendergreen) exhibit resistance to the pea weevil (Bruchus pisorum). A proteomic analysis was carried out to compare seeds from GM pea lines expressing the bean αAI1 protein and the corresponding αAI1‐free segregating lines and non‐GM parental line to identify unintended alterations to the proteome of GM peas due to the introduction of the gene for αAI1. Proteomic analysis showed that in addition to the presence of αAI1, 33 other proteins were differentially accumulated in the αAI1‐expressing GM lines compared with their non‐GM parental line and these were grouped into five expression classes. Among these 33 proteins, only three were found to be associated with the expression of αAI1 in the GM pea lines. The accumulation of the remaining 30 proteins appears to be associated with Agrobacterium‐mediated transformation events. Sixteen proteins were identified after MALDI‐TOF‐TOF analysis. About 56% of the identified proteins with altered accumulation in the GM pea were storage proteins including legumin, vicilin or convicilin, phaseolin, cupin and valosin‐containing protein. Two proteins were uniquely expressed in the αAI1‐expressing GM lines and one new protein was present in both the αAI1‐expressing GM lines and their αAI1‐free segregating lines, suggesting that both transgenesis and transformation events led to demonstrable changes in the proteomes of the GM lines tested.
Proteomic analysis from haploid and diploid embryos of Quercus suber L. identifies qualitative and quantitative differential expression patterns

Quercus suber L. is a Mediterranean forest species with ecological, social and economic value. Clonal propagation of Q. suber elite trees has been successfully obtained from in vitro‐derived somatic and gametic embryos. These clonal lines play a main role in breeding and genetic studies of Q. suber. To aid in unravelling diverse genetic and biological unknowns, a proteomic approach is proposed. The proteomic analysis of Q. suber somatic and gametic in vitro culture‐derived embryos, based on DIGE and MALDI‐MS, has produced for the first time proteomic data on this species. Seventeen differentially expressed proteins have been identified which display significantly altered levels between gametic and somatic embryos. These proteins are involved in a variety of cellular processes, most of which had been neither previously associated with embryo development nor identified in the genus Quercus. Some of these proteins are involved in stress and pollen development and others play a role in the metabolism of tannins and phenylpropanoids, which represent two of the major pathways for the synthesis of cork chemical components. Furthermore, the augmented expression levels found for specific proteins are probably related to the homozygous state of a doubled‐haploid sample. Proteins involved in synthesis of cork components can be detected at such early stages of development, showing the potential of the method to be useful in searching for biomarkers related to cork quality.
The algebra of integro‐differential operators on a polynomial algebra

We prove that the algebra 𝕀n:=K〈 x1,…,xn,∂∂x1,…,∂∂xn,∫1,…,∫n 〉 of integro‐differential operators on a polynomial algebra is a prime, central, catenary, self‐dual, non‐Noetherian algebra of classical Krull dimension n and of Gelfand–Kirillov dimension 2n. Its weak homological dimension is n, and n, ⩽ gldim(𝕀n) ⩽ 2n. All the ideals of 𝕀n are found explicitly, there are only finitely many of them (at most 22n ), they commute (𝔞𝔟= 𝔞𝔟) and are idempotent ideals (𝔞2 = 𝔞). The number of ideals of 𝕀n is equal to the Dedekind number 𝔡n. An analogue of Hilbert's Syzygy Theorem is proved for 𝕀n. The group of units of the algebra 𝕀n is described (it is a huge group). A canonical form is found for each integro‐differential operator (by proving that the algebra 𝕀n is a generalized Weyl algebra). All the mentioned results hold for the Jacobian algebra 𝔸n (but GK (𝔸n) = 3n, note that 𝕀n ⊂ 𝔸n). It is proved that the algebras 𝕀n and 𝔸n are ideal equivalent.
Spectral theoretic characterization of the massless Dirac operator

We consider an elliptic self‐adjoint first‐order differential operator acting on pairs (2‐columns) of complex‐valued half‐densities over a connected compact three‐dimensional manifold without boundary. The principal symbol of our operator is assumed to be trace‐free. We study the spectral function which is the sum of squares of Euclidean norms of eigenfunctions evaluated at a given point of the manifold, with summation carried out over all eigenvalues between zero and a positive λ. We derive an explicit two‐term asymptotic formula for the spectral function as λ to + ∞, expressing the second asymptotic coefficient via the trace of the subprincipal symbol and the geometric objects encoded within the principal symbol‐metric, torsion of the teleparallel connection and topological charge. We then address the question: is our operator a massless Dirac operator on half‐densities? We prove that it is a massless Dirac operator on half‐densities if and only if the following two conditions are satisfied at every point of the manifold: (a) the subprincipal symbol is proportional to the identity matrix; and (b) the second asymptotic coefficient of the spectral function is zero.
Ulnar Impaction Syndrome: Ulnar Shortening vs. Arthroscopic Wafer Procedure

Abstract The outcome of ulnar shortenings was compared with that of arthroscopic wafer resections for ulnar impaction (or abutment) syndrome in patients with a positive ulnar variance. The outcome was measured by DASH score, visual analog scale for pain, and working incapacity. The mean DASH score in the ulnar shortening group was 26; in the wafer group it was 36. The VAS scores were respectively 4.4 and 4.6. The working incapacity was 7? months in the ulnar shortening group and 6.1 months in the wafer group. The differences between the two groups were not statistically significant.
A novel two-dimensional Cd(II) coordination polymer: poly[aqua[μ₄-2-(4-carboxylatobenzoyl)benzoato]cadmium(II)].

The title Cd(II) coordination framework, [Cd(C15H8O5)(H2O)]n or [Cd(bpdc)(H2O)]n [H2bpdc is 2-(4-carboxybenzoyl)benzoic acid], has been prepared and characterized using IR spectroscopy, elemental analysis, thermal analysis and single-crystal X-ray diffraction. Each Cd(II) centre is six-coordinated by two O atoms from one 2-(4-carboxylatobenzoyl)benzoate (bpdc(2-)) ligand in chelating mode, three O-donor atoms from three other bpdc(2-) anions and one O atom from a coordinated water molecule in an octahedral coordination environment. Two crystallographically equivalent Cd(II) cations are bridged by one O atom of the 2-carboxylate group of one bpdc(2-) ligand and by both O atoms of the 4-carboxylate group of a second bpdc(2-) ligand to form a binuclear [(Cd)2(O)(OCO)] secondary building unit. Adjacent secondary building units are interlinked to form a one-dimensional [Cd(OCO)2]n chain. The bpdc(2-) ligands link these rod-shaped chains to give rise to a complex two-dimensional [Cd(bpdc)]n framework with a 4,4-connected binodal net topology of point symbol {4(3). 6(2). 8}. The compound exhibits a strong fluorescence emission and typical ferroelectric behaviour in the solid state at room temperature.
Temporal proteomic analysis of IGF‐1R signalling in MCF‐7 breast adenocarcinoma cells

Dysregulation of the insulin‐like growth factor 1 receptor signalling network is implicated in tumour growth and resistance to chemotherapy. We explored proteomic changes resulting from insulin‐like growth factor 1 stimulation of MCF‐7 adenocarcinoma cells as a function of time. Quantitative analysis using iTRAQ™ reagents and 2‐D LC‐MS/MS analysis of three biological replicates resulted in the identification of 899 proteins (p≤0.05) with an estimated mean false‐positive rate of 2.6%. Quantitative protein expression was obtained from 681 proteins. Further analysis by supervised k‐means clustering identified five temporal clusters, which were submitted to the FuncAssociate server to assign overrepresented gene ontology terms. Proteins associated with vesicle transport were significantly overrepresented. We further analyzed our data set for proteins showing temporal significance using the software, extraction and analysis of differential gene expression, resulting in 20 significantly and temporally changing proteins (p≤0.1). These significant proteins play roles in, among others, altered glucose metabolism (lactate dehydrogenase A and pyruvate kinase M1/M2) and cellular stress (nascent polypeptide‐associated complex subunit α and heat shock (HSC70) proteins). We used multiple reaction monitoring to validate these interesting proteins and have revealed several differences in relative peptide expression corresponding to protein isoforms and variants.
Interaction of recombinant CanPIs with Helicoverpa armigera gut proteases reveals their processing patterns, stability and efficiency

Six diverse representative Capsicum annuum (common name: hot pepper; Solanaceae) protease inhibitor genes, viz CanPI‐5, ‐7, ‐13, ‐15, ‐19, and 22 comprising 1–4 inhibitory repeat domains (IRDs), were cloned and expressed in Pichia pastoris. The recombinant proteins were evaluated for their interactions with bovine trypsin, chymotrypsin, and Helicoverpa armigera gut proteases (HGP) using electrophoretic (native and denaturing) and mass spectrometric (MALDI‐TOF‐MS in combination with intensity fading assays) techniques. These techniques allow qualitative and semiquantitative analysis of multiple and processed IRDs of purified recombinant Capsicum annuum proteinase inhibitor (rCanPI) proteins. rCanPIs showed over 90% trypsin inhibition, varying chymotrypsin inhibition depending on the number of respective IRDs and over 60% inhibition of total HGP. rCanPI‐15 that has only one IRD showed exceptionally low inhibition of these proteases. Interaction studies of rCanPIs with proteases using intensity fading‐MALDI‐TOF‐MS revealed gradual processing of multi‐IRD rCanPIs into single IRD forms by the action of HGP at the linker region, unlike their interactions with trypsin and chymotrypsin. Intensity fading‐MALDI‐TOF‐MS assay showed that CanPI‐13 and ‐15, possessing single IRD and expressed predominantly in stem tissue are degraded by HGP; indicating their function other than defense. In vitro and in vivo studies on rCanPI‐5 and ‐7 showed maximum inhibition of HGP isoforms and their processed IRDs were also found to be stable in the presence of HGP. Even single amino acid variations in IRDs were found to change the HGP specificity like in the case of HGP‐8 inhibited only by IRD‐12. The presence of active PI in insect gut might be responsible for changed HGP profile. rCanPI‐5 and ‐7 enhanced HGP‐7, reduced HGP‐4, ‐5, ‐10 expression and new protease isoforms were induced. These results signify isoform complexity in plant PIs and insect proteases.
Rapid transcriptome and proteome profiling of a non‐model marine invertebrate, Bugula neritina

Non‐model organisms represent the majority of life forms in our planet. However, the lack of genetic information hinders us to understand the unique biological phenomena in non‐model organisms at the molecular level. In this study, we applied a tandem transcriptome and proteome profiling on a non‐model marine fouling organism, Bugula neritina. Using a 454 pyrosequencing platform with the updated titanium reagents, we generated a total of 48M bp transcriptome data consisting of 131 450 high‐quality reads. Of these, 122 650 reads (93%) were assembled to produce 6392 contigs with an average length of 538 bases and the remaining 8800 reads were singletons. Of the total 15 192 unigenes, 13 863 ORFs were predicated, of which 6917 were functionally annotated based on gene ontology and eukaryotic orthologous groups. Subsequent proteome analysis identified and quantified 882 proteins from B. neritina. These results would provide fundamental and important information for the subsequent studies of molecular mechanism in larval biology, development, antifouling research. Furthermore, we demonstrated, for the first time, the combined use of two high‐throughput technologies as a powerful approach for accelerating the studies of non‐model but otherwise important species.
Perfusion pressure and blood flow determine microvascular apparent viscosity

What is the central question of this study? The aim was to evaluate the effect of perfusion pressure on blood flow in small arterioles. The hypothesis was that blood flow regulates the thickness of the red‐cell‐free layer and, therefore, blood flow determines blood apparent viscosity and local vascular resistance in vascular networks with limited myogenic or metabolic regulation of blood flow. What is the main finding and its importance? Reduced perfusion pressures lowered volumetric flow rates and increased local vascular resistance, due to increased blood apparent viscosity. Thus, the local vascular resistance of small arterioles with limited myogenic or metabolic regulation of blood flow, appeared to be determined by changes in blood rheology rather than blood vessel diameter.
Influence of contractile force on the architecture and morphology of the quadriceps femoris

What is the central question of this study? Does contraction influence the fascicle length, pennation angle and effective physiological cross‐sectional area (effPCSA) of the quadriceps femoris muscle? Is there a stronger relationship between effPCSA and maximal strength if effPCSA is measured during maximal contraction rather than at rest? What is the main finding and its importance? Fascicle length decreased, pennation angle increased and effPCSA increased in a non‐linear manner with isometric torque. The effPCSA during maximal contraction and rest were correlated in a similar manner to maximal strength. The effPCSA at rest is sufficient to characterize the muscle size–strength relationship.