Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic diversity and relationships among sorghum accessions using SSRs and RAPDs

Two DNA-based fingerprinting techniques, simple sequence repeats (SSR) and random amplified polymorphic DNA (RAPD) analyses, were applied in sorghum germplasm analysis to compare suitability for quantifying genetic diversity. Twenty-two sorghum genotypes, representing an array of germplasm sources with important agronomic traits, were assayed for polymorphism using 32 RAPD primers and 28 sets of sorghum SSR primers. The results indicated that SSR markers were highly polymorphic with an average of 4.5 alleles per primer. The RAPD primers were less polymorphic with nearly 40% of the fragments being monomorphic. An analysis of genetic diversity among sorghum lines indicated that the genetic distances calculated from SSR data were highly correlated with the distances based on the geographic origin and race classifications. Based on the results of these studies, SSR markers appear to be particularly useful for the estimation of genetic similarity among diverse genotypes of sorghum. Key words : cluster, diversity, polymorphism, RAPD, Sorghum, SSR. African Journal of Biotechnology Vol.2(10) 2003: 334-340
Molecular composition of biogenic secondary organic aerosols using ultrahigh resolution mass spectrometry: comparing laboratory and field studies

Abstract. Numerous laboratory experiments have been performed in an attempt to mimic atmospheric secondary organic aerosol (SOA) formation. However, it is still unclear how close the aerosol particles generated in laboratory experiments resemble atmospheric SOA with respect to their detailed chemical composition. In this study, we generated SOA in a simulation chamber from the ozonolysis of α-pinene and a biogenic volatile organic compound (BVOC) mixture containing α- and β-pinene, Δ3-carene, and isoprene. The detailed molecular composition of laboratory-generated SOA was compared with that of background ambient aerosol collected at a boreal forest site (Hyytiala, Finland) and an urban location (Cork, Ireland) using direct infusion nanoelectrospray ultrahigh-resolution mass spectrometry. Kendrick mass defect and van Krevelen approaches were used to identify and compare compound classes and distributions of the detected species. The laboratory-generated SOA contained a distinguishable group of dimers that was not observed in the ambient samples. The presence of dimers was found to be less pronounced in the SOA from the BVOC mixtures when compared to the one component precursor system. The molecular composition of SOA from both the BVOC mixture and α-pinene represented the overall composition of the ambient sample from the boreal forest site reasonably well, with 72.3 ± 2.5% (n = 3) and 69.1 ± 3.0% (n = 3) common ions, respectively. In contrast, large differences were found between the laboratory-generated BVOC samples and the ambient urban sample. To our knowledge this is the first direct comparison of molecular composition of laboratory-generated SOA from BVOC mixtures and ambient samples.
The Molecular Basis for Species-specific Activation of Human TRPA1 Protein by Protons Involves Poorly Conserved Residues within Transmembrane Domains 5 and 6*

Background: Extracellular acidosis mediates pain and inflammation by activating sensory afferent neurons. Results: Protons activate and sensitize human TRPA1 in a strongly species-specific manner encoded by transmembrane domains 5 and 6. Conclusion: Our data identify TRPA1 as an ion channel likely to mediate acid-induced pain in humans. Significance: Protons are the first known endogenous agonists of TRPA1 with species-specificity for human TRPA1. The surveillance of acid-base homeostasis is concerted by diverse mechanisms, including an activation of sensory afferents. Proton-evoked activation of rodent sensory neurons is mainly mediated by the capsaicin receptor TRPV1 and acid-sensing ion channels. In this study, we demonstrate that extracellular acidosis activates and sensitizes the human irritant receptor TRPA1 (hTRPA1). Proton-evoked membrane currents and calcium influx through hTRPA1 occurred at physiological acidic pH values, were concentration-dependent, and were blocked by the selective TRPA1 antagonist HC030031. Both rodent and rhesus monkey TRPA1 failed to respond to extracellular acidosis, and protons even inhibited rodent TRPA1. Accordingly, mouse dorsal root ganglion neurons lacking TRPV1 only responded to protons when hTRPA1 was expressed heterologously. This species-specific activation of hTRPA1 by protons was reversed in both mouse and rhesus monkey TRPA1 by exchange of distinct residues within transmembrane domains 5 and 6. Furthermore, protons seem to interact with an extracellular interaction site to gate TRPA1 and not via a modification of intracellular N-terminal cysteines known as important interaction sites for electrophilic TRPA1 agonists. Our data suggest that hTRPA1 acts as a sensor for extracellular acidosis in human sensory neurons and should thus be taken into account as a yet unrecognized transduction molecule for proton-evoked pain and inflammation. The species specificity of this property is unique among known endogenous TRPA1 agonists, possibly indicating that evolutionary pressure enforced TRPA1 to inherit the role as an acid sensor in human sensory neurons.
Rapid determination of benzo(a)pyrene in processed meat and fish samples by second-derivative constant-energy synchronous fluorescence spectrometry

A simple, rapid and cost-effective method has been established for the determination of the quantity of benzo(a)pyrene (BaP), one of the most carcinogenic polycyclic aromatic hydrocarbons (PAHs), in roasted, smoked and charcoal grilled foods. Second-derivative constant-energy synchronous fluorescence spectrometry (DCESFS) improves the spectral resolution and selectivity of the fluorescence method. By using this method, processed meat, fish and some other food samples were analysed without resorting to complex pre-separation and purification procedures. The method was found to have a recovery of 97.7% ± 4.3%. The limit of detection (LOD) for BaP was 0.14 µg kg–1, far below the regulatory limit (1.0 µg kg–1) for BaP in food samples specified by the European Union. A certified reference material (Coconut oil, BCR®-458) was used to confirm the validity of the proposed method. The results suggest that the measurements are in a good agreement with the certified BaP concentrations (5.4% deviation). The results obtained by the proposed method for analysing BaP in food samples correlated well with those obtained by GC/MS.
Structural characterization of the N‐terminal autoregulatory sequence of phenylalanine hydroxylase

Phenylalanine hydroxylase (PAH) is activated by its substrate phenylalanine, and through phosphorylation by cAMP‐dependent protein kinase at Ser16 in the N‐terminal autoregulatory sequence of the enzyme. The crystal structures of phosphorylated and unphosphorylated forms of the enzyme showed that, in the absence of phenylalanine, in both cases the N‐terminal 18 residues including the phosphorylation site contained no interpretable electron density. We used nuclear magnetic resonance (NMR) spectroscopy to characterize this N‐terminal region of the molecule in different stages of the regulatory pathway. A number of sharp resonances are observed in PAH with an intact N‐terminal region, but no sharp resonances are present in a truncation mutant lacking the N‐terminal 29 residues. The N‐terminal sequence therefore represents a mobile flexible region of the molecule. The resonances become weaker after the addition of phenylalanine, indicating a loss of mobility. The peptides corresponding to residues 2–20 of PAH have different structural characteristics in the phosphorylated and unphosphorylated forms, with the former showing increased secondary structure. Our results support the model whereby upon phenylalanine binding, the mobile N‐terminal 18 residues of PAH associate with the folded core of the molecule; phosphorylation may facilitate this interaction.
Qualitative exploration of a client-centered, goal-directed approach to community-based occupational therapy for adults with traumatic brain injury.

OBJECTIVES We explored the clinical application of goal-directed therapy in community-based rehabilitation from the perspective of clients with traumatic brain injury (TBI), their significant others, and their treating occupational therapists. METHOD Twelve people with TBI and their significant others completed an outpatient, goal-directed, 12-week occupational therapy program. Semistructured interviews with 12 participants, 10 significant others, and 3 occupational therapists involved in delivering the therapy programs explored their experiences of goal-directed therapy. RESULTS Participants, their significant others, and therapists described goal-directed therapy positively, expressing satisfaction with progress made. CONCLUSION Goals provide structure, which facilitates participation in rehabilitation despite the presence of barriers, including reduced motivation and impaired self-awareness. A therapist-facilitated, structured, goal-setting process in which the client, therapist, and significant others work in partnership can enhance the process of goal setting and goal-directed rehabilitation in a community rehabilitation context.
p53 suppression partially rescues the mutant phenotype in mouse models of DiGeorge syndrome

Significance The 22q11.2 deletion is the most common known genetic cause of congenital heart disease (CHD). The haploinsufficiency of TBX1 has been identified as the cause of CHD. Using mouse models of the disease, we found that reduced dosage of p53 suppresses the Tbx1 mutant phenotype. Tbx1 and p53 proteins coregulate the gene Gbx2, which is required for cardiovascular development. Gbx2 expression is positively regulated by Tbx1, whereas suppression of p53 results in reduced levels of the repressive chromatin mark H3K27me3 at a genetic element occupied by both Tbx1 and p53. These data illustrate a mechanism by which reduced p53, by genetic or pharmacological means, can counterbalance the consequences of reduced dosage of Tbx1. T-box 1 (Tbx1), a gene encoding a T-box transcription factor, is required for embryonic development in humans and mice. Half dosage of this gene in humans causes most of the features of the DiGeorge or Velocardiofacial syndrome phenotypes, including aortic arch and cardiac outflow tract abnormalities. Here we found a strong genetic interaction between Tbx1 and transformation related protein 53 (Trp53). Indeed, genetic ablation of Trp53, or pharmacological inhibition of its protein product p53, rescues significantly the cardiovascular defects of Tbx1 heterozygous and hypomorphic mutants. We found that the Tbx1 and p53 proteins do not interact directly but both occupy a genetic element of Gbx2, which is required for aortic arch and cardiac outflow tract development, and is a known genetic interactor of Tbx1. We found that Gbx2 expression is down-regulated in Tbx1+/− embryos and is restored to normal levels in Tbx1+/−;Trp53+/− embryos. In addition, we found that the genetic element that binds both Tbx1 and p53 is highly enriched in H3K27 trimethylation, and upon p53 suppression H3K27me3 levels are reduced, along with Ezh2 enrichment. This finding suggests that the rescue of Gbx2 expression in Tbx1+/−;Trp53+/− embryos is due to reduction of repressive chromatin marks. Overall our data identify unexpected genetic interactions between Tbx1 and Trp53 and provide a proof of principle that developmental defects associated with reduced dosage of Tbx1 can be rescued pharmacologically.
E(cid:30)cient Reasoning about Finite Satis(cid:28)ability of UML Class Diagrams with Constrained Generalization Sets

UML class diagrams play a central role in the design and speci(cid:28)cation of software, databases and ontologies. The model driven architecture approach emphasizes the central role that models play, towards achieving reliable software. It is important that models are correct and that problems are detected as early as possible in the software de-sign process. However, current case tools do not support reasoning tasks about class diagrams and enable the construction of erroneous models. There is an urgent need for methods for detecting analysis and design problems. In this paper, we present a linear programming based method for reasoning about (cid:28)nite satis(cid:28)ability of UML class diagrams with constrained generalization sets. The method is simple and e(cid:30)cient and can be easily added to a case tool. It improves over existing methods that require exponential resources and extends them to new elements of class diagrams.
A distributed coverage algorithm for multi-UAV with average Voronoi partition

In this paper, we propose a distributed coverage algorithm for a group of UAVs to cover a convex region with average Voronoi partition which aims to ensure the areas of all Voronoi partitions are identical. The proposed algorithm iteratively updates the Voronoi partition through local information exchange with neighbors, and then moves along the computed direction. Different from existing results, the proposed algorithm could make the area difference infinitely small in theory to achieve indeed average area coverage. Simulation results are provided to illustrate the effectiveness of the proposed algorithm.
“It was hard work every session”: Therapists’ view of successful psychoanalytic treatments

ABSTRACT Objective: To explore therapists’ experiences of the therapeutic process in successful cases of psychoanalytic psychotherapy. Method: A two-stage, mixed-method design was used. Sixteen successful cases were drawn from a sample of 92 young adults in psychoanalytic psychotherapy according to Jacobson’s criteria for reliable and clinically significant improvement. Therapist interviews at baseline and termination were analyzed applying Inductive Thematic Analysis. Results: Three core themes emerged: Being Particularly Motivated to be This Patient’s Therapist, Maintaining a Safe and Attentive Therapeutic Position, and Assiduous Work Every Session. The therapists experienced positive feelings towards the patient from the outset of treatment and described active, relational work that included paying attention to incongruities in the patient’s self-presentation and being mindful of patient’s avoidant behavior. The therapist’s motivation and attentive position made it possible to balance support and challenge in the therapeutic relationship. Conclusions: Successful therapeutic work presupposes positive expectations, an active therapeutic stance and assiduous work session-by-session. Therapist expertise may involve the ability to mobilize and work effectively with patient-specific resources and obstacles from the beginning of treatment. In addition to identifying the characteristics and actions of effective therapists, research should also focus on processes emerging within effective therapeutic dyads. Clinical or methodological significance of this article: Our study indicates several factors that seem to characterize therapist expertise and can inform psychotherapy training. Successful therapeutic work presupposes positive expectations, an active therapeutic stance, courage to challenge the patient, and assiduous work session-by-session. Therapist expertise may involve the ability to mobilize and work effectively with patient-specific resources and obstacles from the beginning of treatment. In addition to identifying the characteristics and actions of effective therapists, research should also focus on processes emerging within effective therapeutic dyads.
Thin, fully depleted monolithic active pixel sensor based on 3D integration of heterogeneous CMOS layers

On the way towards fast, radiation tolerant and ultra thin CMOS radiation sensors, we propose new generation of devices based on commercial availability of vertical integration of several CMOS wafers (3D Electronics). In this process, each wafer may be thinned down to about 10 microns end equipped with through-silicon vias (TSV) allowing for electrical interconnection between wafers at a very small pitch (few microns) and with a minimum material budget. The proposed prototype device is a 245×245 pixel array with a pitch of 20 μm, providing active area of 5×5 mm2. In the first silicon layer charge sensing diode and first stage buffer amplifier (source follower) are integrated, using CMOS process on high resistivity epitaxial wafers. Outputs of buffer voltage amplifiers are vertically coupled (through a poly-poly capacitor) to the following stage of processing electronics (charge integration, time continuous shaping and signal discrimination), placed in the second silicon layer (0.13 micron CMOS). The third silicon layer (also 0.13 micron CMOS) is used for implementation of digital (binary) readout with a fast, data driven, self-triggering data flow. After description of the proposed 3D device, an update of results from ongoing tests with the first CMOS MAPS prototype fabricated using high-resistivity epitaxial substrate is provided.
Lactulose Breath Testing Does Not Discriminate Patients With Irritable Bowel Syndrome From Healthy Controls

INTRODUCTION:Recent reports suggest that abnormalities of lactulose breath testing (LBT) are common in patients with irritable bowel syndrome (IBS), although the criteria for abnormal studies are poorly validated, and controlled comparisons are limited. The goal of this study was to determine the prevalence of abnormal LBT using the previously published criteria in both IBS patients and healthy controls, as well as to determine the prevalence and symptom association with methane (CH4) and hydrogen (H2) productions during LBT.METHODS:Consecutive LBT from patients meeting Rome II criteria for IBS and healthy control subjects were examined. Patients listed their most bothersome digestive symptom at the start of the test. LBT was performed using 10 g of lactulose mixed in 240 mL of water, and breath samples collected every 20 min for a 180-min period. Both breath H2 and CH4 were measured. LBT was considered positive if it met any of the previously published criteria: (a) breath H2 of >20 parts per million (ppm), (b) increase in breath H2 in <90 min, (c) dual H2 peaks (12-ppm increase over baseline with a decrease of ≥5 ppm before 2nd peak), and (d) breath CH4 of >1 ppm.RESULTS:In total, 224 patients with IBS and 40 controls were studied. Twenty percent of IBS patients were CH4(+) compared with 15% of controls. CH4(+) IBS patients were significantly more likely than CH4(−) IBS patients to have constipation, and significantly less likely to have diarrhea; however, the association did not hold for symptoms of bloating or pain. Patients and controls did not differ significantly with respect to the frequency of a positive study defined by increase in breath H2 in <90 min (121 per 180 vs 26 per 40, P = 0.79), increase in breath H2 of >20 ppm (92 per 180 vs 24 per 40, P = 0.31), or dual peaks (25 per 180 vs 9 per 40, P = 0.17). CONCLUSIONS:The majority of patients with IBS and healthy subjects meet criteria for an “abnormal” LBT using previously published test criteria, and groups are not discriminated using this diagnostic method. Similarly, while CH4 production was associated with constipation among IBS patients, the prevalence of CH4-positive subjects did not significantly differ between IBS patients and controls. The utility of LBT, in its current form as a diagnostic tool in IBS requires critical reappraisal.
The Discrete Logarithm problem in the ElGamal cryptosystem over the abelian group U(n) Where n= p^m, or 2p^m

This study is mainly about the discrete logarithm problem in the ElGamal cryptosystem over the abelian group U(n) where n is one of the following forms p^m, or 2p^m where p is an odd large prime and m is a positive integer. It is another good way to deal with the ElGamal Cryptosystem using that abelian group U(n)={x: x is a positive integer such that x<n and gcd(n,x)=1} in the setting of the discrete logarithm problem . Since I show in this paper that this new study maintains equivalent (or better) security with the original ElGamal cryptosystem(invented by Taher ElGamal in 1985)[1], that works over the finite cyclic group of the finite field. It gives a better security because theoretically ElGamal Cryptosystem with U(p^m) or with U(2p^m) is much more secure since the possible solutions for the discrete logarithm will be increased, and that would make this cryptosystem is hard to broken even with thousands of years.
Ear Contour Detection Based on Edge Tracking

Ear detection is an important step in ear recognition, the quality of detection will directly affect the final recognition rate . According to the feature of ear and its position on the side face, a method based on edge-tracking is adopted for human ear localization from side face images. Firstly binary image was generated using an adaptive threshold, then outer ear was divided into three regions. Binary image was combined with original image to find the contour of the three regions and the information of ear's position in side face. Experimental results show that the method is simple, its localization accuracy is high, and ear contour edge extracted is clear, connected and non-disturbed
A food-grade industrial arming yeast expressing β-1,3-1,4-glucanase with enhanced thermal stability

The aim of this work was to construct a novel food-grade industrial arming yeast displaying β-1,3-1,4-glucanase and to evaluate the thermal stability of the glucanase for practical application. For this purpose, a bi-directional vector containing galactokinase (GAL1) and phosphoglycerate kinase 1 (PGK1) promoters in different orientations was constructed. The β-1,3-1,4-glucanase gene from Bacillus subtilis was fused to α-agglutinin and expressed under the control of the GAL1 promoter. α-galactosidase induced by the constitutive PGK1 promoter was used as a food-grade selection marker. The feasibility of the α-galactosidase marker was confirmed by the growth of transformants harboring the constructed vector on a medium containing melibiose as a sole carbon source, and by the clear halo around the transformants in Congo-red plates owing to the expression of β-1,3-1,4-glucanase. The analysis of β-1,3-1,4-glucanase activity in cell pellets and in the supernatant of the recombinant yeast strain revealed that β-1,3-1,4-glucanase was successfully displayed on the cell surface of the yeast. The displayed β-1,3-1,4-glucanase activity in the recombinant yeast cells increased immediately after the addition of galactose and reached 45.1 U/ml after 32-h induction. The thermal stability of β-1,3-1,4-glucanase displayed in the recombinant yeast cells was enhanced compared with the free enzyme. These results suggest that the constructed food-grade yeast has the potential to improve the brewing properties of beer.
The K-user interference channel: Strong interference regime

This paper presents a solution for one of the open problems in network information theory: “What is the generalization of the strong interference regime to the K-user interference channel? ” A new approach is developed based on which one can obtain strong interference regimes not only for the multi-user interference channels but also for other interference networks with any arbitrary topology. To this development, some new lemmas are proved which have a central role in our derivations. As a result, this paper establishes the first non-trivial capacity result for the general multi-user classical interference channel (for both discrete and Gaussian channels).