Miracle-dz/UniFAR-FTUs huggingface dataset:
In silico analysis of Plasmodium species specific UvrD helicase

Malaria is still a devastating disease caused by the mosquito-transmitted parasite Plasmodium, particularly Plasmodium falciparum. During the last few years the situation has worsened in many ways, mainly due to malarial parasites becoming increasingly resistant to several anti-malarial drugs. Thus there is an urgent need to find alternate ways to control malaria and therefore it is necessary to identify new drug targets and new classes of anti-malarial drugs. A malaria vaccine would be the ultimate weapon to fight this deadly disease but unfortunately despite encouraging advances a vaccine is not likely soon. DNA helicases from the PcrA/UvrD/Rep (PUR) subfamily are important for the survival of the various organisms, mainly pathogenic bacteria. Members from this subfamily can be targeted and inhibited by a variety of synthetic compounds. Using bioinformatics analysis we have shown that UvrD from this subfamily is the only member present in the P. falciparum genome, while PcrA and Rep are absent in the genome. UvrD from the parasite shows no homology to any protein or enzyme from human and thus can be considered as a strong potential drug target. In the present study we report an in silico analysis of this important enzyme from a variety of Plasmodium species. The results suggest that among all the species of Plasmodium, P. falciparum contains the largest UvrD and this enzyme is variable at the sequence and structural level.
Social Anxiety Modulates Risk Sensitivity through Activity in the Anterior Insula

Decision neuroscience offers the potential for decomposing differences in behavior across individuals into components of valuation intimately tied to brain function. One application of this approach lies in novel conceptualizations of behavioral attributes that are aberrant in psychiatric disorders. We investigated the relationship between social anxiety and behavior in a novel socially determined risk task. Behaviorally, higher scores on a social phobia inventory (SPIN) among healthy participants were associated with an increase in risky responses. Furthermore, activity in a region of the dorsal anterior insula (dAI) scaled in proportion to SPIN score in risky versus non-risky choices. This region of the insula was functionally connected to areas in the intraparietal sulcus and anterior cingulate cortex that were related to decision-making across all participants. Overall, social anxiety was associated with decreased risk aversion in our task, consistent with previous results investigating risk taking in many everyday behaviors. Moreover, this difference was linked to the anterior insula, a region commonly implicated in risk attitudes and socio-emotional processes.
Practising what they preach? An investigation into the pedagogical beliefs and online teaching practices of National Teaching Fellows

National Teaching Fellows (NTFs) in the UK are celebrated individuals who have made a successful claim for teaching excellence to the Higher Education Academy. This paper reports the results of an empirical study of NTFs with expertise in online learning, which measured their pedagogical beliefs and online teaching practices, using a ‘teaching conceptions’ model. Given the growth of online teaching within higher education, this paper seeks to establish whether excellent teachers ‘practise what they preach’ in online environments and can support other less able colleagues in developing their online practices.
Risk factors associated with bacteriological cure, new infection, and incidence of clinical mastitis after dry cow therapy with three different antibiotics

Factors affecting bacteriological cure rates (BCR) and new intramammary infections (IMI) during the dry period as well as clinical mastitis (CM) during early lactation were investigated in 414 German Holstein dairy cows receiving dry cow therapy. Cows were treated with either benethamine benzylpenicillin (300,000 IU), penethamate hydriodide (100,000 IU), and framycetin sulphate (100 mg, n = 136), or cefquinome (150 mg, n = 135), or benzathine cloxacillin (1,280 mg, n = 143). Overall BCR, IMI, and CM at parturition were 86.4%, 20.7%, and 4.3%, respectively. The three antibiotic treatments differed only in BCR, with cloxacillin yielding better results than the others. Udder quarters from cows with > 4 lactations had a higher risk of IMI and CM at calving. Chronic changes in udder tissues were linked to a lower BCR and were associated with a higher risk of CM during early lactation. The risk of CM at calving was higher in udder quarters with unspecific or subclinical mastitis before drying off. In conclusion, with antibiotic dry cow therapy, age and health status of the udder appear to be major determinants of IMI and CM during the dry period and early lactation, while BCR was associated with the antibiotic type and udder tissue status.
Thickness Mapping of the Occipital Bone on CT-data -- a New Approach Applied on OH 9

A new approach for the analysis of cranial bone thickness is introduced. The study focuses on the occipital bone of modern humans and of a 1.25 Myr-old H. ergaster/erectus specimen from Olduvai Gorge (OH 9). A semiautomatic algorithm detects a multitude of thicknesses from CT-data of the investigated bones. We find that every bone is characterized by its own distribution pattern of cranial thickness, which is then analyzed statistically. The results demonstrate that the thickness distribution of the occipital bone of OH 9 is within the normal range of the H. sapiens sample (which itself shows a remarkably high variance). This contributes to a further analysis of phyletic differences of hominid morphology by including distribution patterns of thickness combined with aspects of functional anatomy.
Reducing the Steiner Problem in a Normed Space

Consider a set P of points in a normed space whose unit sphere is a d-dimensional symmetric polytope with 2d extreme points. This paper proves that there always exists a Steiner minimum tree whose Steiner points are located only at points whose coordinates appear in points of P. This generalizes a recent result of Snyder on d-dimensional rectilinear space, which itself extends Hanan’s well-known and much quoted result on the rectilinear plane. Furthermore, the proof in this paper is much simpler than Snyder’s proof, even considerably shorter than Hanan’s proof. A consequence of this result is that the Steiner problem for P in such a space is reduced to a Steiner problem on graphs and is solvable by any existing Steiner graph algorithms. The paper also conjectures that such a reduction is impossible if the polytope has more than $2d$ extreme points and provides partial support for the conjecture.
Targeted lung expression of interleukin-11 enhances murine tolerance of 100% oxygen and diminishes hyperoxia-induced DNA fragmentation.

Acute lung injury is a frequent and treatment-limiting consequence of therapy with hyperoxic gas mixtures. To determine if IL-11 is protective in oxygen toxicity, we compared the effects of 100% O 2 on transgenic mice that overexpress IL-11 in the lung and transgene ( 2 ) controls. IL-11 markedly enhanced survival in 100% O 2 with 100% of transgene ( 2 ) animals dying within 72–96 h and . 90% of transgene ( 1 ) animals surviving for more than 10 d. This protection was associated with markedly diminished alveolar-capillary protein leak, endothelial and epithelial membrane injury, lipid peroxidation, and pulmonary neutrophil recruitment. Significant differences in copper zinc superoxide dismutase and catalase activities were not noted and the levels of total, reduced and oxidized glutathione were similar in transgene ( 1 ) and ( 2 ) animals. Glutathione reductase, glutathione peroxidase, and manganese superoxide dismutase activities were slightly higher in transgene ( 1 ) as versus ( 2 ) mice after 100% O 2 exposure, and IL-11 diminished hyperoxiainduced expression of IL-1 and TNF. Hyperoxia also caused cell death with DNA fragmentation in the lungs of transgene ( 2 ) animals and IL-11 markedly diminished this cell death response. These studies demonstrate that IL-11 markedly diminishes hyperoxic lung injury. They also demonstrate this protection is associated with small changes in lung antioxidants, diminished hyperoxia-induced IL-1 and TNF production, and markedly suppressed hyperoxia-induced DNA fragmentation. ( J. Clin. Invest. 1998. 101:1970–1982.)
Crystalline silicon solar cells beyond 20% efficiency

This paper describes a fabrication process to obtain high efficiency c-Si cells (> 20%) based on the Laser Fired Contact Passivated Emitter Rear Cell (LFC-PERC) concept. Photovoltaic efficiencies beyond 20% have been achieved using thermal SiO2 as a rear passivation layer on 2 cm × 2 cm solar cells with 0.45 Qcm Fz c-Si substrates. Efficiencies up to 22% are expected for material resistivities in the 0.4–5 Ωcm using an optimized rear contact grid.
Design of Wide Passband/Stopband Microstrip Bandpass Filters With the Stepped Coupled Line

Novel wide passband microstrip bandpass filters with broader stopbands are provided in this paper. The proposed bandpass filters are composed of the stepped coupled line and two short-circuited stubs. The electrical length of the stepped coupled line is a quarter of wavelength so that the proposed filter is compact size. Moreover, the stepped coupled line with weak-strong-weak coupling results in a wide stopband. Furthermore, with short-circuited stubs connected at the input/output port, there is a steeper passband skirt and broader passband. In addition, the agreement between theoretical prediction and measurement validates our proposed structure.
Violapyrones H and I, New Cytotoxic Compounds Isolated from Streptomyces sp. Associated with the Marine Starfish Acanthaster planci

Two new α-pyrone derivatives, violapyrones H (1) and I (2), along with known violapyrones B (3) and C (4) were isolated from the fermentation broth of a marine actinomycete Streptomyces sp. The strain was derived from a crown-of-thorns starfish, Acanthaster planci, collected from Chuuk, Federated States of Micronesia. The structures of violapyrones were elucidated by the analysis of 1D and 2D NMR and HR-ESIMS data. Violapyrones (1–4) exhibited cytotoxicity against 10 human cancer cell lines with GI50 values of 1.10–26.12 μg/mL when tested using sulforhodamine B (SRB) assay. This is the first report on the cytotoxicity of violapyrones against cancer cell lines and the absolute configuration of violapyrone C.
Genes Encoding Oxidase Components Activity by Down-Regulating Expression of Adenine Dinucleotide Phosphate Oxidase Inhibits Human Phagocyte Nicotinamide Dexamethasone But Not Indomethacin

We investigated the effects of dexamethasone or indomethacin on the NADPH oxidase activity, cytochrome b 558 content, and expression of genes encoding the components gp91- phox and p47- phox of the NADPH oxidase system in the human monocytic THP-1 cell line, differentiated with IFN- g and TNF- a , alone or in combination, for up to 7 days. IFN- g and TNF- a , alone or in combination, caused a signiﬁcant up-regulation of the NADPH oxidase system as reﬂected by an enhancement of the PMA-stimulated superoxide release, cytochrome b 558 content, and expression of gp91- phox and p47- phox genes on both days 2 and 7 of cell culture. Noteworthy was the tremendous synergism between IFN- g and TNF- a for all studied parameters. Dexamethasone down-regulated the NADPH oxidase system of cytokine-differentiated THP-1 cells as assessed by an inhibition on the PMA-stimulated superoxide release, cytochrome b 558 content, and expression of the gp91- phox and p47- phox genes. The nuclear run-on assays indicated that dexamethasone down-regulated the NADPH oxidase system at least in part by inhibiting the transcription of gp91- phox and p47- phox genes. Indomethacin inhibited only the PMA-stimulated superoxide release of THP-1 cells differentiated with IFN- g and TNF- a during 7 days. None of the other parameters was affected by indomethacin. We conclude that dexamethasone down-regulates the NADPH oxidase system at least in part by inhibiting the expression of genes encoding the gp91- phox and p47- phox components of the NADPH oxidase system. The Journal
Problems with Existing Procedures to Calculate Exact Unconditional P‐Values for Non‐Inferiority/Superiority and Confidence Intervals for Two Binomials and How to Resolve Them

Recently several papers have been published that deal with the construction of exact unconditional tests for non‐inferiority and confidence intervals based on the approximative unconditional restricted maximum likelihood test for two binomial random variables. Soon after the papers have been published the commercially available software for exact tests StatXact has incorporated the new methods. There are however gaps in the proofs which since have not been resolved adequately. Further it turned out that the methods for testing non‐inferiority are not coherent and test for non‐inferiority can easily come to different conclusions compared to the confidence interval inclusion rule. In this paper, a proposal is made how to resolve the open problems. Berger and Boos (1994) developed the confidence interval method for testing equality of two proportions. StatXact (Version 5) has extended this method for shifted hypotheses. It is shown that at least for unbalanced designs (i.e. largely different sample sizes) the Berger and Boos method can lead to controversial results. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interrogating functional integration between injected pluripotent stem cell-derived cells and surrogate cardiac tissue

Myocardial infarction resulting in irreversible loss of cardiomyocytes (CMs) remains a leading cause of heart failure. Although cell transplantation has modestly improved cardiac function, major challenges including increasing cell survival, engraftment, and functional integration with host tissue, remain. Embryonic stem cells (ESCs), which can be differentiated into cardiac progenitors (CPs) and CMs, represent a candidate cell source for cardiac cell therapy. However, it is not known what specific cell type or condition is the most appropriate for transplantation. This problem is exasperated by the lack of efficient and predictive strategies to screen the large numbers of parameters that may impact cell transplantation. We used a cardiac tissue model, engineered heart tissue (EHT), and quantitative molecular and electrophysiological analyses, to test transplantation conditions and specific cell populations for their potential to functionally integrate with the host tissue. In this study, we validated our analytical platform using contractile mouse neonatal CMs (nCMs) and noncontractile cardiac fibroblasts (cFBs), and screened for the integration potential of ESC-derived CMs and CPs (ESC-CMs and -CPs). Consistent with previous in vivo studies, cFB injection interfered with electrical signal propagation, whereas injected nCMs improved tissue function. Purified bioreactor-generated ESC-CMs exhibited a diminished capacity for electrophysiological integration; a result correlated with lower (compared with nCMs) connexin 43 expression. ESC-CPs, however, appeared able to appropriately mature and integrate into EHT, enhancing the amplitude of tissue contraction. Our results support the use of EHT as a model system to accelerate development of cardiac cell therapy strategies.
Relevance of class, molecular weight and isoelectric point in predicting human light chain amyloidogenicity

The ability to predict the amyloidogenicity of certain light chains may facilitate an earlier diagnosis of AL amyloidosis and, possibly, lead to more effective treatment. Using current methods, available in clinical chemistry laboratories, we assessed the class, the relative molecular mass (Mr) and the isoelectric point of urinary monoclonal light chains from 35 patients with AL amyloidosis (A +) and 51 without amyloidosis (A –). The light chain class (LCC) was λ in 77% and 45% of A + and A – patients, respectively. Light chain fragments (LCF) with low Mr (12–18 x 103 were detected in the urine of 30/35 A + patients and in 15/51 A – ones. The mean (SD) isoelectric point (pI) of A + light chains was 4.8 (1.1) while in A – patients it was 6.2 (1.6). Univariate analysis showed significant differences between the two groups for the three parameters. Discriminant analysis gave a function which allowed a correct allocation of 81% of the cases between the two groups.
Unsupervised WSD with a Dynamic Thesaurus *

Diana McCarthy et al. (ACL-2004) obtain the predominant sense for an ambiguous word based on a weighted thesaurus of words related to the ambiguous word. This thesaurus is obtained using Dekang Lin’s (COLING-ACL1998) distributional similarity method. Lin averages the distributional similarity by the whole training corpus; thus the list of words related to a given word in his thesaurus is given for a word as type and not as token, i.e., does not depend on a context in which the word occurred. We observed that constructing a list similar to Lin’s thesaurus but for a specific context converts the method by McCarthy et al. into a word sense disambiguation method. With this new method, we obtained a precision of 69.86%, which is even 7% higher than the supervised baseline.
Generation of multiple orbital angular momentum (OAM) Modes with a circularly polarized multimode patch antenna

The helical wave that carries orbital angular momentum has received much attention due to its potential in communications and other aspects. In this paper, a multimode concentric circularly polarized patch antenna is designed to generate multiple orbital angular momentum modes. The proposed antenna consists of three circularly polarized patches, one circular patch and two shorted annular ring patches, all in the same layer. Each circularly polarized patch corresponds to one OAM state respectively. All three patches are designed to operate at 2.45 GHz. The simulated electric field and radiation property are also presented.
Collaborative Planning by Two Groups of Student Teachers

This study used Doyle's academic task framework to examine whether and in what ways a collaborative planning task (designing a 30-minute lesson in reading comprehension) directed student teachers' attention to reading comprehension and promoted problem solving. Ethnographic procedures were used to examine 6 student teachers' (2 groups of 3) interactions and written evaluations of their experience, focusing on 5 aspects of the task: (1) the lesson plan; (2) subtasks of the planning process; (3) content of interactions; (4) student teachers' thinking; and (5) student teachers' perceptions of their learning. Analysis revealed that each group developed a different instructional plan, although both worked to understand the dimension of reading comprehension under consideration (inferring causes when effects are explicitly stated) and to design a detailed instructional plan for promoting that dimension. Student teachers discussed numerous instructional activities. Various levels of thinking were observed as student teachers specified, elaborated, and evaluated each others' proposals. Student teachers generally perceived the collaborative environment as productive and supportive, although analysis of negative responses suggested the importance of trust as a feature of the task environment. Finally, the task framework was found to be a reasonable tool for studying the academic work of prospective teachers.
Evaluation of Prime/Boost Regimens Using Recombinant Poxvirus/Tyrosinase Vaccines for the Treatment of Patients with Metastatic Melanoma

Purpose: Two clinical trials were conducted to evaluate the clinical efficacy and immunologic impact of vaccination against the tyrosinase protein plus systemic interleukin 2 (IL-2) administration in patients with advanced metastatic melanoma. Experimental Design: Full-length tyrosinase was employed as an immunogen to induce diverse immunologic responses against a commonly expressed melanoma antigen. Heterologous prime/boost vaccination with recombinant vaccinia and fowlpox vectors encoding tyrosinase was first explored in a randomized three-arm phase II trial, in which vaccines were administered alone or concurrently with low-dose or high-dose IL-2. In a subsequent single cohort phase II trial, all patients received the same vaccines and high-dose IL-2 sequentially rather than concurrently. Results: Among a total of 64 patients treated on these trials, 8 objective partial responses (12.5%) were observed, all in patients receiving high-dose IL-2. Additional patients showed evidence of lesional regression (mixed tumor response) or overall regression that did not achieve partial response status (minor response). In vitro evidence of enhanced immunity against tyrosinase following protocol treatments was documented in 3 of 49 (6%) patients tested serologically, 3 of 23 (13%) patients tested for T-cell recognition of individual tyrosinase peptides, and 4 of 16 (25%) patients tested for T-cell recognition of full-length tyrosinase protein with real-time reverse transcription-PCR techniques. Conclusions: Whereas prime/boost immunization with recombinant vaccinia and fowlpox viruses enhanced antityrosinase immunity in some patients with metastatic melanoma, it was ineffective alone in mediating clinical benefit, and in combination with IL-2 did not mediate clinical benefit significantly different from that expected from treatment with IL-2 alone.
Interpersonal Distance in Immersive Virtual Environments

Digital immersive virtual environment technology (IVET) enables behavioral scientists to conduct ecologically realistic experiments with near-perfect experimental control. The authors employed IVET to study the interpersonal distance maintained between participants and virtual humans. In Study 1, participants traversed a three-dimensional virtual room in which a virtual human stood. In Study 2, a virtual human approached participants. In both studies, participant gender, virtual human gender, virtual human gaze behavior, and whether virtual humans were allegedly controlled by humans (i.e., avatars) or computers (i.e., agents) were varied. Results indicated that participants maintained greater distance from virtual humans when approaching their fronts compared to their backs. In addition, participants gave more personal space to virtual agents who engaged them in mutual gaze. Moreover, when virtual humans invaded their personal space, participants moved farthest from virtual human agents. The advantages and disadvantages of IVET for the study of human behavior are discussed.
Automatic Modulation Recognition of Communication Signals.

The project is aimed at designing an intelligent communication system where the receiver is able to detect the modulation scheme of the signal it receives using Automatic Modulation Recognition (AMR) algorithms, without having minimum or no prior knowledge of the transmitted signal. Six digital modulation schemes namely QPSK, BPSK, 2ASK, 4ASK, 2FSK, 4FSK and 16QAM were used. Algorithms based on deriving key statistical features from the communication signal, were formed. Features were also extracted using Azzouz and Nandi‟s techniques. Neural Networks were applied to the extracted features to distinguish between signals having different modulation schemes. The simulations were performed for different SNR values as well as different number of neurons in a one and two hidden layers.
Chemotaxis of human neutrophils and monocytes induced by Cryptococcus neoformans

Chemotaxis of human neutrophils and monocytes was stimulated by sera activated with greater than or equal to 1.25 x 10(6) Cryptococcus neoformans. Leukocytes from five renal transplant recipients had depressed chemotactic responses to C. neoformans-activated sera when compared with normal subjects (P less than 0.05). Concentrations of cryptococcal capsular polysaccharide less than 1 mg/ml failed to generate chemotactic factors from sera.