Miracle-dz/UniFAR-FTUs huggingface dataset:
From pull-down data to protein interaction networks and complexes with biological relevance

MOTIVATION Recent improvements in high-throughput Mass Spectrometry (MS) technology have expedited genome-wide discovery of protein-protein interactions by providing a capability of detecting protein complexes in a physiological setting. Computational inference of protein interaction networks and protein complexes from MS data are challenging. Advances are required in developing robust and seamlessly integrated procedures for assessment of protein-protein interaction affinities, mathematical representation of protein interaction networks, discovery of protein complexes and evaluation of their biological relevance. RESULTS A multi-step but easy-to-follow framework for identifying protein complexes from MS pull-down data is introduced. It assesses interaction affinity between two proteins based on similarity of their co-purification patterns derived from MS data. It constructs a protein interaction network by adopting a knowledge-guided threshold selection method. Based on the network, it identifies protein complexes and infers their core components using a graph-theoretical approach. It deploys a statistical evaluation procedure to assess biological relevance of each found complex. On Saccharomyces cerevisiae pull-down data, the framework outperformed other more complicated schemes by at least 10% in F(1)-measure and identified 610 protein complexes with high-functional homogeneity based on the enrichment in Gene Ontology (GO) annotation. Manual examination of the complexes brought forward the hypotheses on cause of false identifications. Namely, co-purification of different protein complexes as mediated by a common non-protein molecule, such as DNA, might be a source of false positives. Protein identification bias in pull-down technology, such as the hydrophilic bias could result in false negatives.
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Aplastic Anemia: A Common Hematological Abnormality Among Peripheral Pancytopenia

Background: Aplastic anemia is a well-recognized form of marrow failure. The incidence of aplastic anemia is subjected to wide variation. Most cases are acquired and immune-mediated but there are also inherited forms. Aim: The study was conducted to assess the magnitude of the problem, morphological changes and determinants of aplastic anemia in North Bengal. Materials and Methods: A cross-sectional study had been conducted for a period of one year among 5 to 70 years age group. Initially complete blood count followed by bone marrow examination was done for diagnosis. Results: Out of 48 cases, 38 (79.17%) had hypocellular diagnosed as aplastic anemia, 5 (10.42%) each had normocellular and hypercellular bone marrow. Histopathology shows that 30 (78.95%) cases had increased iron stores in bone marrow and 8 (21.05%) cases had decreased iron stores. Subjects less than 20 years of age mostly (31.58%) suffered from non-severe disease in contrast to subjects in higher age groups who had severe or very severe disease, though the trend was not significantly different (χ2 for linear trend 0.171, P > 0.05). Conclusion: The study shows aplastic anemia is a common hematological abnormality among peripheral pancytopenia in North Bengal region where males were affected more than females.
Geometrical calibration and aperture configuration design in multi-pinhole SPECT

A clinical gamma camera can be converted into a high resolution SPECT system for small animal imaging, by replacing the clinical collimator(s) with pinhole collimators. However, for optimal performance, an accurate geometrical calibration is required. If it is assumed that the detector orbit is a true circle, the calibration requires the determination of seven parameters. It has been shown that these can be uniquely determined from a SPECT scan of a phantom consisting of three point sources, if two of the distances between these point sources are known. For multi-pinhole SPECT, two point sources should be sufficient, knowledge of the distance between the point sources is not required. The calibration method has been extended for cases where the orbit deviates from the ideal circle. A second interesting problem in multi- pinhole SPECT is the optimisation of the collimator design. This requires a measure of image quality, enabling objective comparison between different designs. An efficient analytical method has been developed for that purpose. With this method, it has been shown that the aperture diameter should be slightly smaller than the desired system resolution. We have also found that increased multiplexing (which comes with an apparent increase in system sensitivity) does not lead to reduced variance for a particular target resolution. In practice, avoiding all overlap seems to yield better performance.
A mikrorespirációs (MicroRespTM) módszer alkalmazása apajpusztai szikes talajok mikrobaközösségeinek katabolikus aktivitás mintázatának vizsgálatára

A talajok hazai es nemzetkozi kutatasaban egyre nagyobb szerepet kap a talajok mikrobiotajanak vizsgalata. Hazai viszonylatban szikes talajokon eddig keves ilyen iranyu kutatas tortent. Kutatasunkban kiskunsagi szikes talajok mikrobakozossegeinek katabolikus aktivitas mintazatat vizsgaltuk Apajpusztarol szarmazo mintakon. A mintavetelhez negy, a szikesedes kulonboző fazisaira jellemző novenyzettel rendelkező teruletet valasztottunk ki (szoloncsak vaksziknovenyzet, kiskunsagi szikfoknovenyzet, urmos szikespuszta es fuves szikespuszta), ezek teruleteről a talaj mikrobiologiai szempontbol legaktivabbnak tekintett 0-10 cm-es reteget mintaztuk. A mintak nehany fontosabb talajtani parameteret meghataroztuk (szemcseosszetetel, pH, so-, humusz- es mesztartalom, valamint nehany fontosabb tapelem mennyisege). A negy elterő novenyzetű terulet kozott a talajtani parametereik alapjan is jelentős kulonbsegeket tapasztaltunk. A mintak mikrobiologiai aktivitasat az itthon meg kevesse ismert mikrorespiracios (MicroRespTM).
Pathogens in COPD exacerbations identified by comprehensive real-time PCR plus older methods

Respiratory infection is a major cause of exacerbation in chronic obstructive pulmonary disease (COPD). Infectious contributions to exacerbations remain incompletely described. We therefore analyzed respiratory tract samples by comprehensive real-time polymerase chain reaction (PCR) in combination with conventional methods. We evaluated multiple risk factors for prolonged hospitalization to manage COPD exacerbations, including infectious agents. Over 19 months, we prospectively studied 46 patients with 50 COPD exacerbations, collecting nasopharyngeal swab and sputum samples from each. We carried out real-time PCR designed to detect six bacterial species and eleven viruses, together with conventional procedures, including sputum culture. Infectious etiologies of COPD exacerbations were identified in 44 of 50 exacerbations (88%). Infections were viral in 17 of 50 exacerbations (34%). COPD exacerbations caused by Gram-negative bacilli, including enteric and nonfermenting organisms, were significantly associated with prolonged hospitalization for COPD exacerbations. Our results support the use of a combination of real-time PCR and conventional methods for determining both infectious etiologies and risk of extended hospitalization.
Wideband Center-fed Stacked Patch Circularly Polarized Antenna used in Phased Array

A center-fed circularly polarized stacked patch antenna (CF-CPSPA) with enhanced axial-ratio (AR) bandwidth is proposed in this paper. The antenna is composed of two microstrip patches, the lower patch consists of a circular pad, an elliptical-ring, and two branch lines connecting them, which is used to realize the center-fed condition, and the upper patch is an elliptical patch to achieve the wide band performance. Firstly, two center-fed linearly polarized stacked patch antennas with wide band are designed, one mode radiated with x polarization, and the other generates y polarized radiation. Next, the orthogonal modes of two linearly polarized antennas are combined together by a specific design. Finally, the approximate equal amplitude and quadrature phase difference of the introduced modes are achieved in the operating frequency band with proper parameters analysis. And the impedance bandwidth and 3dB AR bandwidth is improved to 30.4% and 16.5%.
Absolute Position Sensing Based on a Robust Differential Capacitive Sensor with a Grounded Shield Window

A simple differential capacitive sensor is provided in this paper to measure the absolute positions of length measuring systems. By utilizing a shield window inside the differential capacitor, the measurement range and linearity range of the sensor can reach several millimeters. What is more interesting is that this differential capacitive sensor is only sensitive to one translational degree of freedom (DOF) movement, and immune to the vibration along the other two translational DOFs. In the experiment, we used a novel circuit based on an AC capacitance bridge to directly measure the differential capacitance value. The experimental result shows that this differential capacitive sensor has a sensitivity of 2 × 10−4 pF/μm with 0.08 μm resolution. The measurement range of this differential capacitive sensor is 6 mm, and the linearity error are less than 0.01% over the whole absolute position measurement range.
Psychosocial Needs Assessment among Earthquake Survivors in Lorestan Province with an Emphasis on the Vulnerable Groups

Introduction: Iran is one of the ten most earthquake prone countries in the world. Earthquakes not only cause new psychological needs among the population but particularly so when one considers vulnerable groups. This in - depth study was conducted with the aim of assessing psychosocial needs six months after an earthquake happened in the west of the county in Lorestan province. Methods: This is a qualitative study using focus group discussion that focuses mainly on the vulnerable groups (women, children, elderly and disabled people) after an earthquake in Boz-azna; a village in Lorestan province in western part of Iran. Findings: Results of the psychosocial assessment indicated feelings of anxiety and worries in four vulnerable groups. Horror, hyper-excitement, avoidance and disturbing thoughts were observed in all groups with the exception of the elderly. Educational failures, loneliness and isolation were highlighted in children. All groups encountered socio-economic needs that included loss of assets and sense of insecurity and also reproductive problems were reported in women's group. Discussion and Conclusion: Modification of a protocol on psychosocial support considering the context of the rural and urban areas with emphasis on the specific needs of the vulnerable groups is an appropriate strategy in crisis management. It seems that appropriate public awareness regarding assistance programs can be effective in reducing stress and needs of disaster survivors.
Modelling binaural detection of speech stimuli in complex reverberant environments

In listening experiments that assess spatial hearing (e.g. localization) in the presence of background noise it is important to ensure audibility of the target stimulus. Target audibility could be easily controlled using knowledge about the masked thresholds in the respective paradigm. However, if a large number of acoustic conditions as well as target sounds are considered, individual psychoacoutic threshold measurements are not feasible and alternative methods need to be applied. In this study a binaural auditory model is applied to predict masked thresholds for wide-band non-stationary stimuli. This model closely follows the approach of Hant and Alwan (Speech Communication, 2003, Vol. 40, pp. 291-313) [7]. In the first stage of the model an auditory front-end generates an internal representation of the stimuli in both ears. The auditory front-end includes head-related transfer functions, auditory bandpass filtering, squaring, temporal integration, logarithmic compression and additive internal noise. In the second stage, a decision device combines d′ information across time, frequency and ears and provides an estimate of the masked threshold. Three different methods of combining information across ears were compared: A better-ear approach, a cross-ear glimpsing approach and an approach using binaural integration. The model was verified using psychoacoustic masked threshold data of a detection paradigm that considered a target word presented from 15 different locations in a reverberant multi-talker background. The model predictions were in very good agreement with the measured masked thresholds. It is concluded that this model is suitable to control audibility of a target stimulus in a complex reverberant environment. Moreover, the model was used to systematically analyze the effect of head-shadow, signal spectrum, auditory sensitivity and room reverberation on target audibility.
The Influence of Plant-Soil Interactions on Plant and Soil Microbial Responses to Nitrogen Deposition

A common response of plant communities to increased nitrogen (N) deposition is a shift in species’ abundances. Multiple factors have been proposed to explain the changes in abundance, notably competition and soil acidification. We hypothesized that a plant species that decreased in abundance with elevated N would have lower ectomycorrhizal fungi, altered root-associated bacteria communities, and/or greater susceptibility to Al toxicity than a species that increased in abundance with increasing N deposition. We examined changes in plant-microbe associations and Al toxicity in two dominant species from an alpine dry meadow community subjected to long-term low-level N addition. Carex rupestris has increased in cover over time with N addition and Kobresia myosuroides has decreased. We conducted field sampling of soil microbes from treatment plots and tested whether field levels of Al have toxic effects on sedge species in a greenhouse study. Declines in ectomycorrhizal infection of Cenococcum geophilum occurred on Kobresia with increasing N treatment. In contrast, neither Al level nor changes in bacteria community composition corresponded with the change in cover of sedge species. Decreased ectomycorrhizal infection may have contributed to the decrease in abundance of Kobresia. This study contributes to an understanding of the types of plant-soil interactions that may influence how plant species respond to N deposition and rejects Al toxicity and changes in bacteria composition as factors that likely play a role in changes in sedge abundance. Introduction Atmospheric nitrogen (N) deposition from anthropogenic sources has led to eutrophication and loss of diversity, followed by acidification in many aquatic and terrestrial ecosystems worldwide (Galloway et al. 2004). While changes in plant diversity is one of the first and most commonly reported
A human IgG-like bispecific antibody co-targeting epidermal growth factor receptor and the vascular endothelial growth factor receptor 2 for enhanced antitumor activity

ABSRTRACT Both Epidermal Growth Factor Receptor (EGFR) and the Vascular Endothelial Growth Factor Receptor 2 (VEGFR2) play critical roles in tumorigenesis. We hypothesized co-targeting EGFR and VEGFR2 using a bispecific antibody might have significant therapeutic potential. Here,we designed and produced a human IgG-like bispecific antibody (Bi-Ab) based on the variable regions of cetuximab (an anti-EGFR antibody) and mAb-04 (an anti-VEGFR2 antibody developed in our lab) . The Bi-Ab was found to inhibit the proliferation, survival and invasion of cancer cells via ablating phosphorylation of receptor and downstream signaling. In vivo efficacy was demonstrated against established HT-29 and SKOV-3 xenografts grown in nude mice. Studies revealed our Bi-Ab was able to restrain xenografted tumor growth and prolong survival of mice through inhibiting cell proliferation,promoting apoptosis and anti-angiogenesis. In contrast to cetuximab or mAb-04 alone, our Bi-Ab exhibits enhanced antitumor activity and has equal or slightly superior activity to their combination (Combi). It shows promise as a therapeutic agent, especially for use against tumors EGFR and/or VEGFR2 over-expressing malignancies.
Data Integration through Clustering and Finding Statistical Relations - Validation of Approach

The paper analyzes an approach to data integration based on finding statistical relations between data. The data used for experimenting comes from surveys collected from student groups. The practical problem that underlies this research is discovering the model of knowledge about students, which would allow for making predictions about their future educational success or failure. The obstacle is that data collected for different groups over years has different format and this makes it difficult to reuse the previously collected data. Thus we had to find a way, to overcome this difficulty and integrate the heterogeneous data. The paper analyzes the feasibility of integrating data using this method. Although based on particular application, the model of computations presented in the paper is of more general nature, and should be applicable in many other domains.
Present‐day deformation of northern Pakistan from Salt Ranges to Karakorum Ranges

Episodic GPS measurements are used to quantify the present-day velocity field in the northwestern Himalaya from the southern Pamir to the Himalayan foreland. We report large postseismic displacements following the 2005 Kashmir earthquake and several mm/yr thrusting of the central segment of the Salt Ranges and Potwar Plateau over the foreland, westward thrusting of Nanga Parbat above the Kohistan Plateau, and ~12 mm/yr SSE velocities of the Karakorum Ranges and of the Deosai and Kohistan Plateaus relative to the Indian Plate. Numerical simulations allow to determine a first approximation of slip along active faults: (1) substantial creep of ~87 mm/yr between 2006 and 2012 along the flat northeast of the Balakot-Bagh Thrust affected by the 2005 earthquake; (2) ~5 mm/yr slip of the central segment of the Salt Ranges and Potwar Plateau, whereas their western boundaries are clearly inactive over the time span covered by our measurements; (3) 13 mm/yr ductile slip along the Main Himalayan Thrust modeled by a dislocation dipping 7° northward, locked at a depth of 15 km; and (4) ~20 mm/yr slip along the shear zone forming the western boundary of Nanga Parbat, between depths of 1.6 and 6.5 km. Residuals velocities suggest the existence of left-lateral strike slip along the Jhelum Fault.
Fast and efficient voltage scheduling by evolutionary slack distribution

To minimize energy consumption by voltage scaling in design of heterogeneous real-time embedded systems, it is necessary to perfom two distinct tasks: task scheduling (TS) and voltage selection (VS). Techniques propased to date either are fast hut yield inetlicient results, or output efficient solutions after many slow iterations. As a core problem to solve in the inner Iwp of a system-level optimization cycle, it is critical that the algorithm he fast while producing high quality results. This paper presents a new technique called EvolutioMry Relative Slack Distribution Voltage Scheduling (ERSD-VS) that achieves both speed and etrciency. It addresses priority adjustment and slack distribution issues with low cost heuristics. Experimental results from running publicly available testhenches show up to 42% energy saving compared to a published technique called EVEN-VS. It also shows up to 70 times speed improvement compared to an efficient technique called EE-GLSA.
Analysis of dynamic frequency response of class E amplifier

A dynamic response of the output voltage to the input supply voltage VDD of a class E amplifier is derived with modeling the circuit by a low-frequency model and a high-frequency model. If the perturbation frequency is much lower than the switching frequency, the state-space averaging model of the class E amplifier can be approximated as a single-pole low-pass filter composed of the choke inductance LRFC and the parallel combination of the switch resistance and the shunt capacitor resistance. The analysis in this paper is based on the steady-state behavior outside the designed conditions given in [2]. Hence, the derivation is applicable even if the class E amplifier is operated in off-tuned conditions. The analytical results for the frequency response of a 1 MHz class E amplifier matched well with Pspice simulations at the perturbation frequency less than 100 kHz.
Geometric Comparison of Clarifications and Rule Sets

We present a technique for evaluating classifications by geometric comparison of rule sets. Rules are represented as objects in an n-dimensional hyperspace. The similarity of classes is computed from the overlap of the geometric class descriptions. The system produces a correlation matrix that indicates the degree of similarity between each pair of classes. The technique can be applied to classifications generated by different algorithms, with different numbers of classes and different attribute sets. Experimental results from a case study in a medical domain are included.
The attitude and competence level of basic school teachers in the teaching of ICT in Cape Coast Metropolis

The use of ICT impacts on almost every facet of our daily activities. Educators and governments have also devoted huge resources to the provision of technology in the learning environment. Despite the increase in ICT tools in Ghana, some teachers do not use them in their teaching. The purpose of this study is to measure the attitude and competence level of basic school teachers in teaching ICT in the Cape Coast Metropolis. The research design used is the descriptive survey design. Stratified sampling technique was used to select 150 teachers for the study. Questionnaire was used as the research instrument in collecting data. Frequency tables, t-test, pie charts, mean and standard deviation were computed by means of SPSS v.20. 0. The study revealed that majority of the teachers have poor attitude towards the teaching of ICT. Even though majority of the teachers have good competency level in Microsoft word and spreadsheets, they, however, lack competence in the use of email. Similarly, most of the teachers lacked training in ICT usage. We recommend that teachers should be given the necessary training in ICT usage so that they become familiar with modern pedagogy in the use of ICT.