Miracle-dz/UniFAR-FTUs huggingface dataset:
A deep learning approach for uncovering lung cancer immunome patterns

Tumor immune cell infiltration is a well known factor related to survival of cancer patients. This has led to deconvolution approaches that can quantify immune cell proportions for each individual. What is missing, is an approach for modeling joint patterns of different immune cell types. We adapt a deep learning approach, deep Boltzmann machines (DBMs), for modeling immune cell gene expression patterns in lung adenocarcinoma. Specifically, a partially partitioned training approach for dealing with a relatively large number of genes. We also propose a sampling-based approach that smooths the original data according to a trained DBM and can be used for visualization and clustering. The identified clusters can subsequently be judged with respect to association with clinical characteristics, such as tumor stage, providing an external criterion for selecting DBM network architecture and tuning parameters for training. We show that the hidden nodes of the trained networks cannot only be linked to clinical characteristics but also to specific genes, which are the visible nodes of the network. We find that hidden nodes that are linked to tumor stage and survival represent expression of T-cell and mast cell genes among others, probably reflecting specific immune cell infiltration patterns. Thus, DBMs, trained and selected by the proposed approach, might provide a useful tool for extracting immune cell gene expression patterns. In the case of lung adenocarcinomas, these patterns are linked to survival as well as other patient characteristics, which could be useful for uncovering the underlying biology.
Protein profiling for phylogenetic relationship in snakehead species

Protein banding pattern of eight snakeheads – Channa species viz., Channa striatus, Channa marulius, Channa punctatus, Channa diplogramme, Channa bleheri, Channa gachua, Channa stewartii and Channa aurantimaculata collected from different regions of India were used to study the phylogenetic relationship among them. The banding pattern from muscle protein indicated a unique profile for each species and the electrophoregrams showed similarities among the species studied. In the SDS-PAGE, a maximum of 12 protein bands were obtained for C. gachua followed by 11 for C. diplogramme and 10 for C. marulius whereas less number of bands were recorded for the remaining species. Molecular weight of the protein bands varied from 16 kDa 232 kDa. UPGMA (Unweighted Pair Group Method with Arithmetic Mean) dendrogram revealed that the phylogenetic relationship was very close among C. aurantimaculata and C. bleheri and also between C. gachua and C. stewarti.
IMPLEMENTATION OF NADHIR ONLINE REGISTRATION SYSTEM IN BADAN WAKAF INDONESIA USING AGILE DEVELOPMENT METHODS

The Indonesian Waqf Board is an independent state institution formed under law number 41 of 2004 concerning endowments. At present, Nadhir registration service activities at the Indonesian Waqf Board are still carried out offline, which causes Nadhir registration service activities to be inefficient and take a long time. From the above problems the authors make research "Implementation of the Nadhir Online Registration System Using Agile Development Methods" which can help the Indonesian Waqf Board in nadhir registration activities in the Indonesian Waqf Board. This research uses agile development methods that focus on personal interactions, software functionality, collaboration with clients, responses to change. The results based on experiment are in the form of a website-based nadhir registration information system that features online registration, file upload, disposition, file verification, recommendations, approving and printing certificates that can help the process of registering Nadhir in Indonesian Waqf Board . System test results obtained from the usability variable of 82% so it can be concluded that the system is feasible to use.
Role of oqxA and oqxB Genes in the Development of Multidrug Resistant Phenotype among Clinical Klebsiella pneumoniae Isolates from Various Cases

This study investigated the prevalence of oqxA and oqxB genes and their effective roles in the development of multidrug resistant (MDR) phenotype among clinical isolates of Klebsiella pneumoniae. Out of 150 clinical samples, 50 (33%) isolates were recognized as K. pneumoniae according to the morphological and biochemical properties. The minimum inhibitory concentrations (MICs) assay revealed that the resistance values of the isolates were 43 (86%) against ceftriaxone (4≥64 μg/ml), 42 (84%) against ceftazidime (16≥64 μg/ml), 41 (82%) against cefepime (≥16 μg/ml), 21 (42%) against ertapenem (≥8 μg/ml), 18 (36%) against imipenem (4≥16 μg/ml), 15 (30%) against ciprofloxacin (≥4 μg/ml), 11 (22%) against levofloxacin (≥8 μg/ml), 45 (90%) against nitrofurantoin (128≥512 μg/ml), 36 (72%) against trimethoprime-sulfamethoxazole (≥320 μg/ml), and 4 (8%) against tigecycline (≥8 μg/ml). Genotype detection revealed that oqxA was found in 48 (96%) of K. pneumoniae isolates, whereas oqxB was found in 6 (12%) isolates. The MDR phenotype was observed in 40 (80%) isolates, of which 38 (95%) were harbored oqxA and/or oqxB genes. DNA sequencing of oqxA revealed the presence of three silent mutations. The phylogenetic tree of oqxA variants showed a significant deviation of these variants from K. pneumoniae species. The high prevalence of oqxA among K. pneumoniae isolates may contribute to the reduction of their susceptibility to multiple antimicrobial agents.
Zinc and selenium as modulating factors of the anatomy and physiology of Billbergia zebrina (Bromeliaceae) during in vitro culture

Deleterious effects induced by high zinc (Zn) concentrations can be alleviated with selenium (Se) co-exposure. Therefore, we analyzed the morphophysiological changes of Billbergia zebrina in response to Zn and Se co-exposure. Plants were cultured in media containing three Zn concentrations (0, 30, and 300 μM) combined with two Se concentrations (0 and 4 μM), for a total of six treatments. At 75 d of culture, the leaf anatomy, chlorophyll (Chl) a fluorescence, and contents of photosynthetic pigments (Chl) and nutrients were analyzed. The total Chl content declined with rising Zn concentrations. Plants cultured with Se presented a decrease in the Chl a/b ratio and greater total Chl content. Positive L- and K-bands were verified under Se absence and with 30 and 300 μM Zn. Plants showed bioaccumulation capacity and tolerance to excess Zn. Se acted as a modulator to alleviate the Zn stress.
A low power read-out integrated circuit for multiple sensors

This paper proposes a low power read-out integrated circuit (ROIC) for multiple sensors having a DC output signal. It comprises a chopper-stabilized instrumentation amplifier (CSIA) followed by a second-order incremental analog-to-digital converter (IADC). The CSIA has a dual-frequency path to effectively eliminate any 1/f noise and offset. A variable gain module (VGM) is also connected to the CSIA to improve its range of potential applications. A CMOS buffer amplifier followed by the CSIA is used to achieve the ROIC’s linearity and drive capability. The back-end of the ROIC has a switched- capacitor IADC to provide a digital output. The correlated double sampling (CDS) technique was used in the IADC’s first integrator to reduce the offset and noise. The combination of these techniques enables the ROIC to achieve an input referred offset of 5 μV and a best error voltage of ±0.01 mV. The ROIC was implemented in 0.18 μm CMOS technology. It occupies an area of approximately 2.56 mm2 and consumes 835 μA of current from a 1.6 V of supply voltage.
An Efficient Invitro Approach for Direct and Callus Mediated Regeneration of Curcuma karnatakensis – An Endemic Plant of Karnataka

ABSTRACT An in vitro protocol for direct and callus mediated regeneration of complete plantlets of Curcuma karnatakensis was established. For direct regeneration rhizome buds were used as explants and culturing them on MS medium supplemented with 2 mgL−1 6-Benzyladenine (BA) resulted with an average of 4.00 ± 0.57 shoots per explant. Callus induction and multiplication study revealed that the percentage of callus induction was better in rhizome explants (68% explants induced callus within 30 d of inoculation) compared to shoot base explants (54% explants induced in 60 d) on MS medium supplemented with 2 mgL−1 2,4-Dichlorophenoxyacetic acid. Rhizome derived calli were used to induce organogenic callus on medium with higher concentration of α-Naphthalene acetic acid (5 mgL−1) and further transferred to regeneration medium containing 0.5 mgL−1 NAA and 4mgL−1 BA which produced 5.33 ± 0.66 shoots per explant in 8 weeks of culture. In vitro regenerated plants were successfully acclimatized to greenhouse conditions with a survival rate of 85% and exhibited normal phenotypes.
Epigenetics Evolution and Replacement Histones: Evolutionary Changesat Drosophila H2AvD

The evolutionary changes in the Drosophila H2A and H2AvD genes, which encode histones, were analyzed using the sequences of 12 Drosophila sp. for understanding the evolution of histone replacement and epigenetics. The Ball gene, coding for a histone threonine kinase, was located head-to-head with the H2AvD gene in seven Drosophila sp. A strongly conserved DNA sequence was also found in the region upstream of the H2AvD gene; this sequence is most likely a transcriptional signal, because the sequence was also conserved in four other Drosophila sp. that did not have an upstream Ball gene. The SPARC gene, coding for a calcium-binding domain, was located tail-to-tail in the region downstream of the H2AvD gene in 11 Drosophila sp. studied. A moderately conserved DNA sequence was found in the H2AvD gene region at the splicing site in the first intron. Different codon usages for the H2A and H2AvD genes were found for 11 of 17 amino acids, and codon usages characteristic of replacement histones (H2AvD, H4r, H3.3A and H3.3B) were found for amino acids. Codon usage was considerably different at several histone modification sites in the H2A gene. These results suggested that unlike the H3.3 and H4r genes, not only post-transcriptional control, but also transcriptional control played a role in the H2AvD gene. In addition to post-transcriptional controls, such as splicing and translation, the development of a control system for transcription must have occurred during the evolution of histone replacement and epigenetic systems.
Hydrothermal synthesis of cerium‐doped Co3O4 nanoflakes as electrode for supercapacitor application

In this work, cerium was doped in various concentrations ranging from 1.0 to 7.0 at. % by means of a facile hydrothermal synthesis route with an intention to improve the capacitive properties of Co3O4. X‐ray powder diffraction (XRD), scanning electron microscopy coupled with energy dispersive X‐ray spectroscopy (EDX) and HRTEM were employed to study the structural characteristics, morphology, elemental constitution and d‐spacing of the synthesized material. The capacitive characteristics were analyzed through cyclic voltammetry (CV), galvanostatic charge‐discharge (GCD) test and electrochemical impedance spectroscopy (EIS). Materials characterizations revealed the formation of pristine and Ce‐doped Co3O4 nanoflakes, and their average size was in the range of 45 to 55 nm and possessing excellent elemental purity. The CV test showed that 5.0 at. % Ce‐doped Co3O4 nanoflakes deliver outstanding specific capacitance, that is, 1309.6 F/g and excellent cyclic stability of 90.86% after 2000 CV cycles at a scan rate 5 mV/s. The GCD test at 1‐10 A/g showed excellent rate capability, that is, 82.87% at high current density of 10 A/g. The EIS test revealed excellent electrical conductivity of the material. Experimental results suggest that Ce‐doped Co3O4 has an outstanding potential for use in energy storage devices.
Plume or bubble? Mixed-convection flow regimes and city-scale circulations

Large-scale circulations around a city are co-modulated by the urban heat island and by regional wind patterns. Depending on these variables, the circulations fall into different regimes ranging from advection-dominated (plume regime) to convection-driven (bubble regime). Using dimensional analysis and large-eddy simulations, this study investigates how these different circulations scale with urban and rural heat fluxes, as well as upstream wind speed. Two dimensionless parameters are shown to control the dynamics of the flow: (1) the ratio of rural to urban thermal convective velocities that contrasts their respective buoyancy fluxes and (2) the ratio of bulk inflow velocity to the convection velocity in the rural area. Finally, the vertical flow velocities transecting the rural to urban transitions are used to develop a criterion for categorizing different large-scale circulations into plume, bubble or transitional regimes. The findings have implications for city ventilation since bubble regimes are expected to trap pollutants, as well as for scaling analysis in canonical mixed-convection flows.
Real, but Limited: A Meta-Analytic Assessment of Framing Effects in the Political Domain

Abstract In the past three decades, scholars have frequently used the concept of framing effects to assess the competence of citizens' political judgments and how susceptible they are to elite influence. Yet prior framing studies have reached mixed conclusions, and few have provided systematic cumulative evidence. This study evaluates the overall efficacy of different types of framing effects in the political domain by systematically meta-analyzing this large and diverse literature. A combined analysis of 138 experiments reveals that when examined across contexts, framing exerts medium-sized effects on citizens' political attitudes and emotions. However, framing effects on behavior are negligible, and small effects are also found in more realistic studies employing frame competition. These findings suggest that although elites can influence citizens by framing issues, their capacity to do so is constrained. Overall, citizens appear to be more competent than some scholars envision them to be.
Government and its aid buildings: the governmental influence on the design and management of China-aided stadium projects after 2000

ABSTRACT The number of China-aided stadium projects has greatly increased since 2000, along with new working models and architectural characteristics. As government-financed construction projects, these stadiums could not escape the influence of the Chinese government. This study aims to explore such influence on the design and management processes of China-aided stadium projects after 2000 and identify their variations and characteristics through an interview-based study using statistical and qualitative text analysis methods. The results show that the governmental influence exists, and various processes received different degrees of influences from the Chinese government, among which the pre-design, design and tender and bid processes receive more. Such influences are generated through various approaches including the official setup of the pre-design process, the requirement to use Chinese building codes (standard), the strict control of investment costs, the compulsory guiding principles for design, and the opacity of the bid evaluation, etc. This research represents new knowledge to link the political aspects with the architectural outcomes, generates references for future oversea projects and concludes to better understand the implementation model of the China-aided construction system.
Vulnerability of a riparian zone towards invasion by alien plants depends on its structure

Abstract Riparian zones support high biodiversity and are among the most vulnerable parts of the landscape. Their degradation facilitates the spread of invasive alien plant species. Our aim was to investigate the relationship between environmental characteristics of riparian zones and distribution and abundance of invasive alien plant taxa (IAT) along three rivers in Slovenia. In 100-m reaches of riparian zone we determined environmental characteristics and the presence and abundance of IAT. Canonical correspondence analysis was used to assess the relationship between IAT and environmental factors. The numbers and abundances of IAT in specific reaches were correlated with environmental factors using Spearman coefficient. These results revealed that the number and abundance of IAT in riparian zone were strongly positively correlated to the distance from river source, while they were negatively correlated with altitude, vegetation structure complexity, completeness of riparian zone and current velocity. Environmental factors that explained the distribution and abundance of IAT significantly were: the altitude, flow dynamics, distance from source, width of riparian zone, land-use, bank and channel structure, water depth and velocity. The research has pointed out the need for proper management of riparian zones to prevent invasion by IAT and also to strengthen other services provided by riparian zone as buffering anthropogenic impacts to water body, stabilising bank structure and increasing biodiversity.
The complete mitochondrial genome sequence of Pelates quadrilineatus (Perciformes: Terapontidae)

Abstract The complete mitochondrial genome of marine fish Pelates quadrilineatus was sequenced by the high throughput sequencing method. This genome was 16,823 bp in length, consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one large non-coding region. The gene arrangement of P. quadrilineatus is identical to those of other fishes. Phylogenetic tree based on 13 protein coding genes shows that Terapontidae has a closer phylogenetic relationship to Pentacerotidae than to Chaetodontidae.
Official Visit, Bank Credit and Maturity Mismatch: Evidence from Chinese Listed Firms

ABSTRACT It is becoming increasingly common in recent years that Chinese government officials visit companies on site and the news about this spread widely on the Internet. Official visits can bring various benefits to companies in China, where the government still plays an important role in allocating economic resources, including bank credit. Based on the data of officials’ visits to Chinese listed firms during 2006–2019, this paper finds that firms’ access to short-term bank loans increases significantly after officials’ visits, which, in turn, significantly enhance the degree of maturity mismatch. Furthermore, the paper finds that the stock market reacts negatively to the maturity mismatch. However, firms’ stock return is discounted less for maturity mismatch both in short and long term when firms are visited by officials. The findings in this paper are helpful in profoundly understanding China’s economic system and Chinese government–enterprise relationship.
Opto-Electrical Investigation of Zn Metal-Doped CdS and Their Application in Soft Lithographic Technique

Un-doped CdS and Zn metal-doped CdS (0.1-0.5 M) were synthesized by chemical precipitation method. Properties like optical band gap and conductivity were determined by different characterization techniques. UV-Visible spectroscopy was applied to estimate the band gap where it showed a significant blue shift due to quantum confinement effect. Size determined by scanning electron microscopy (SEM) was found to be in nanorange from 41 to 60 nm for both un-doped and metal doped CdS nanocrystals. EDAX confirmed the doping by showing peak for Zn. XRD (X-ray diffraction) showed the lattice structure to be cubic for the synthesized nanoparticles and conductivity for un-doped CdS was 7.69E-6 Ω-1m-1 where it changes to 9.25E-6 Ω-1m-1 and 7.98E-6 Ω-1m-1 for 0.2 M and 0.5 M Zn-doped CdS, respectively. In order to obtain good results, nanocrystals having highest conductivity are used in soft lithographic technique. Here μTM (micro transfer-molding) was followed for patterning with PDMS (poly-(dimethylsiloxane)) mold and silicon substrate for better results.
On the integration of acoustic phase-gradient metasurfaces in aeronautics

Metamaterials might be one of the breakthrough technologies needed from the aeronautic industry to achieve the more and more challenging targets set by the international authorities, especially about noise emissions. In this article, a theoretical link between Transformation Acoustics and Generalized Snell’s Law, two widely used metamaterial models, is demonstrated analytically and applied to case studies. The relevance of the connection in the aeroacoustic field is discussed along with the consequent computational advantages for numerical simulations. This is exploited to perform a simulation-based design optimization of a phase-graded metasurface acoustic lining of a 2 D duct in presence of flow. Results show promising abilities of the optimized device to modify and control the directivity of the noise emitted from the duct by means of unconventional reflections. The noise reduction in the desired direction is obtained through constructive and destructive interference, with no absorption from the boundaries.
Field Experiment on the Profit Implications of Merchants' Discretionary Power to Override Data-Driven Decision-Making Tools

Data-driven decision-making (DDD) is rapidly transforming modern operations. The availability of big data, advances in data analytics tools, and rapid gains in processing power enable firms to make decisions based on data rather than intuition. Yet, most firms still allow managers to override decisions from DDD tools, as managers might possess private information not present in the DDD tool. We report on a field-experiment conducted by an automobile replacement parts retailer that examines the profit implications of providing discretionary power to merchants. We find that merchants’ overrides of the DDD tool reduce profitability by 5.77%. However, our analysis over product life cycle (PLC) reveals that merchants increase (decrease) profitability for growth- (mature- & decline-) stage products. This paper was accepted by Charles Corbett, operations management.
Towards Digital Multigrade One-room Schoolhouses for Underprivileged Communities in Rural Pakistan

Context matters in the design and development of educational opportunities. Despite extensive global efforts to make education accessible for all, one out of every five children are outof-school. The situation demands re-thinking of learning strategies, particularly in underprivileged contexts. Continued advancements in learning technologies may offer novel solutions. The one-room schoolhouse is a centuries-old proven educational system, which has yielded promising results for rural areas. Using a multigrade teaching method, the one-room schoolhouse provides a resilient model for educating children where school administration faces typical issues of remote and rural areas such as lack of quality teachers, fewer children in each level, low socio-economic status of parents, lack of rooms in a school building, etc. This paper reports a case study of an integrated approach to teaching out-of-school children in rural Pakistan using education technology in a one-room schoolhouse environment using a multigrade teaching method. The paper (1) synthesizes the knowledge of practice and research on one-room schoolhouses, multigrade teaching, and education technology developments; (2) reports the on-ground practices of multigrade one-room schoolhouses in a real-life scenario in rural Pakistan and integrating digital capabilities into these schoolhouses; and (3) proposes the ways to implement and scale this method to educate out-of-school children in other underprivileged communities. Cite as Badar, F. , Mason, J. (2020) Towards Digital Multigrade One-room Schoolhouses for Underprivileged Communities in Rural Pakistan. Computer-Based Learning in Context, 2(1), 21-39. DOI: 10.5281/zenodo.4057844