Miracle-dz/UniFAR-FTUs huggingface dataset:
Economic and Diagnostic Biomarker Tests of Neonatal Sepsis: A Prospective Study from a Tertiary Care Hospital in a Low-Income Country

Background Neonatal sepsis is a leading cause of morbidity and mortality in low-and middle-income countries (LMICs). There are several sophisticated biomarkers; however, they are still insufficient in precision. In this perspective, our study aims to search for a pragmatic diagnostic biomarker in the age category. Methods A cross-sectional study was conducted over six months(April-September 2018). All neonates with a diagnosis of probable sepsis were included. Logistic regression analysis of demographic variables was done to elucidate any association with confirmed sepsis cases. The median with interquartile range (IQR)] and mean with standard deviation (SD) were calculated, and then compared. The area under the receiver operating characteristic curve (AUROC) of the commonly opted biomarker tests [distribution width of red blood cells (RDW) and platelets(PDW), mean platelet volume(MPV), C-reactive protein (CRP), erythrocyte sedimentation rate (ESR)] was compared to the culture-confirmed case. Results Of the 171 suspected sepsis subjects, we discovered a significant burden of newborn sepsis, with 18.7% of cases being culture-confirmed. 66 Early-onset sepsis(EOS) and 105 Late-onset sepsis(LOS) probable sepsis cases were enrolled. A higher incidence was revealed among male infants 24(14%) compared to females 8(4.7%). On logistic regression analysis, preterm birth [odds ratio (OR): 10.9, 95% confidence interval (CI): 4.5-26.9] and low birth weight (OR: 6.5, 95% CI: 2.4-17.9) were significantly associated. Coagulase-negative Staphylococcus aureus (CoNS) (n =6) among gram-positive, and Pseudomonas aeruginosa (n =6) was among gram-negative, were the leading etiologies. Escherichia coli (n =3) was the predominant bacteria in EOS subjects, while Pseudomonas aeruginosa (n =6) among LOS. Median interquartile range(IQR): platelet count 144.5(99-192), red cell distribution width 18(16.9-20), CRP 6(3-18.3); and mean ± SD: MPV (11.7 ± 1.7); PDW (15.2 ± 3.5) were attained, among confirmed cases. The AUROC, of biomarker tests was attained in the order: PDW(0.86) > MPV(0.81) > RDW(0.76) > CRP(0.67) > ESR(0.59); similarly, the cut-off order was >11.2, >10.4, >16.8, >2.9, >4.5, respectively. Conclusions Our finding shows an increment in the width and volume of RBCand platelet: RDW, MPV, and PDW have a diagnostic role in neonatal sepsis.
A New Role of NAP1L1 in Megakaryocytes and Human Platelets

Platelets (PLTs) are anucleate and considered incapable of nuclear functions. Contrastingly, nuclear proteins were detected in human PLTs. For most of these proteins, it is unclear if nuclear or alternatively assigned functions are performed, a question we wanted to address for nuclear assembly protein 1 like 1 (NAP1L1). Using a wide array of molecular methods, including RNAseq, co-IP, overexpression and functional assays, we explored expression pattern and functionality of NAP1L1 in PLTs, and CD34+-derived megakaryocytes (MKs). NAP1L1 is expressed in PLTs and MKs. Co-IP experiments revealed that dihydrolipolylysine-residue acetyltransferase (DLAT encoded protein PDC-E2, ODP2) dynamically interacts with NAP1L1. PDC-E2 is part of the mitochondrial pyruvate-dehydrogenase (PDH) multi-enzyme complex, playing a crucial role in maintaining cellular respiration, and promoting ATP-synthesis via the respiratory chain. Since altered mitochondrial function is a hallmark of infectious syndromes, we analyzed PDH activity in PLTs from septic patients demonstrating increased activity, paralleling NAP1L1 expression levels. MKs PDH activity decreased following an LPS-challenge. Furthermore, overexpression of NAP1L1 significantly altered the ability of MKs to form proplatelet extensions, diminishing thrombopoiesis. These results indicate that NAP1L1 performs in other than nucleosome-assembly functions in PTLs and MKs, binding a key mitochondrial protein as a potential chaperone, and gatekeeper, influencing PDH activity and thrombopoiesis.
Fluctuation of the Carrier-Envelope Phase of a Few-Cycle Laser Pulse from a Chirped-Pulse Amplification System with the Gas Pressure in a Hollow Fiber

We experimentally confirmed that additional CEP fluctuations induced in a hollow fiber increased with gas pressure. A gas pressure in the hollow fiber of between 2 and 2.5 atm results in both a short-pulse generation and the small CEP fluctuation. We also measured the carrier-envelope phase (CEP) fluctuations of spectrally broadened intense pulses that passed through a hollow fiber. An additional carrier-envelope phase fluctuation of 0.12 rad was induced in white light generated in the hollow fiber under the optimum gas pressure.
A new family for the enigmatic sea pen genus Gyrophyllum Studer, 1891 (Octocorallia, Pennatulacea), a molecular and morphological approach

The description in 1891 of the sea pen genus Gyrophyllum Studer, 1891 and also the type species G. hirondellei Studer, 1891 was based on a single colony collected in the Azores Archipelago. During the 19th and 20th centuries, the family placement of this genus became controversial as the set of morphological features present in Gyrophyllum could justify its assignation to both the families Pennatulidae Ehrenberg, 1834 and Pteroeididae Kölliker, 1880. Deliberations over this intermediate set of characters finally ended in the reunification of the genera and species of both families under Pennatulidae by principle of priority. The use of molecular sources of information based on a series of sequencing techniques presents a different but promising phylogenetic scenario in order to go further in the understanding of pennatulacean systematics. In this paper, a complementary morphological and molecular study (multiloci sequences with three mitochondrial and one nuclear markers) based mainly on newly collected material is carried out. This study re-confirms from a molecular point of view previously published results that indicate the position of Gyrophyllum as being distant from Pennatula Linnaeus, 1758 and Pteroeides Herklots, 1858 (type genera of the families Pennatulidae and Pteroeididae, respectively). This fact together with the results of a detailed morphological examination strongly supports the placement of the enigmatic genus Gyrophyllum in a separate family: Gyrophyllidae fam. nov. and resolves the nomenclatural uncertainty at family level for this genus. Moreover, the characters previously considered useful in the distinction of the two currently recognised species G. hirondellei in the Atlantic and G. sibogae Hickson, 1916 in the Indo-western Pacific are revisited.
Rhizosphere bacterial and fungal communities of healthy and wilted pepper (Capsicum annuum L.) in an organic farming system

ABSTRACT: Rhizosphere microorganisms play an important role in the growth and health of plants. Around the world, diverse soil-borne pathogens attack Capsicum annuum causing significant damage and economic losses. This study determined whether the diversity and composition of microbial communities in the rhizosphere soil of C. annuum plants is significantly changed by wilt disease. We used the 16S rRNA gene for bacteria and the internal transcribed spacer region for fungi to characterize the rhizosphere microbiomes of healthy and wilted plants. The most abundant bacterial phyla were Proteobacteria and Gemmatimonadetes, while the most abundant fungal phyla were Ascomycota and Mucoromycota. The bacterial α-diversity did not show significant differences in richness and diversity, but did show a significant difference in evenness and dominance of species. Rare taxa were present in both healthy and wilted conditions with relative abundances < 1%. In the fungi, all evaluated estimators showed a significant reduction in the wilted condition. The β-diversity showed significant differences in the structure of bacterial and fungal communities, which were segregated according to plant health conditions. The same occurred when comparing the alpha and beta diversity of this study based on organic agriculture with that of other studies based on conventional agriculture. We observed a significant difference with estimators analyzed by segregating rhizosphere communities depending on the farming method used. Finally, the differential abundance analysis did not show significant results in the bacterial communities; however, in the fungal communities, Fusarium, Thanatephorus, Rhizopus, Curvularia, Cladosporium, and Alternaria were more abundant in the rhizosphere of wilted than healthy plants. Species from these genera have been previously reported as phytopathogens of several plants, including C. annuum.
Novel trends in affinity biosensors: current challenges and perspectives

Molecular biorecognition processes facilitate physical and biochemical interactions between molecules in all crucial metabolic pathways. Perhaps the target analyte and the biorecognition element interactions have the most impactful use in biosensing applications. Traditional analytical sensing systems offer excellent biorecognition elements with the ability to detect and determine the presence of analytes. High affinity antibodies and DNA play an important role in the development of affinity biosensors based on electrochemical, optical and mass sensitive approaches. Advancements in this area routinely employ labels, label free, nanoparticles, multifunctional matrices, carbon nanotubes and other methods to meet the requirements of its own application. However, despite increasing affinity ceilings for conventional biosensors, the field draws back in meeting specifically important demands, such as long-term stability, ultrasensitivity, rapid detection, extreme selectivity, strong biological base, calibration, in vivo measurements, regeneration, satisfactory performance and ease of production. Nevertheless, recent efforts through this line have produced novel high-tech nanosensing systems such as ‘aptamers’ and ‘phages’ which exhibit high-throughput sensing. Aptamers and phages are powerful tools that excel over antibodies in sensibility, stability, multi-detection, in vivo measurements and regeneration. Phages are superior in stability, screening for affinity-based target molecules ranging from small to proteins and even cells, and easy production. In this review, we focus mainly on recent developments in affinity-based biosensors such as immunosensors, DNA sensors, emphasizing aptasensors and phage-based biosensors basing on novel electrochemical, optical and mass sensitive detection techniques. We also address enzyme inhibition-based biosensors and the current problems associated with the above sensors and their future perspectives.
Can geosynchronous imaging Fourier transform spectrometer capture vertical and temporal variability of a convective atmosphere?

Insufficient high vertical and temporal resolution data have limited the precipitation forecast skill of convective initiation. The Geosynchronous Imaging Fourier Transform Spectrometer (GIFTS), a new hyperspectral geostationary satellite measurement system, could provide top-of-atmosphere (TOA) radiances across two broad spectral regions with high-resolutions in spectral, horizontal and temporal spaces within a fixed domain. A set of modeled and observed vertical profiles of atmospheric moisture and temperature during a convective initiation (CI) event within the observing period of the International H2O Project (IHOP_2002) are used to assess the potential values of GIFTS measurements to convective precipitation forecast. First, it is shown that the model simulation captures reasonably well the movement of the precipitation bands and the gradient structures of temperature and water vapor of the convectively initiated storm. Second, the observed vertical and temporal variability of water vapor during the CI period is shown to be quite significant in the lower troposphere. The differences between observations and model simulation are also noticed. Using both the observed and the model-predicted profiles as input to GIFTS radiative transfer model (RTM), it is finally shown that the simulated GIFTS radiance could capture the high vertical and temporal variability of the real and modeled atmosphere prior to the CI, as well as the differences between observations and model forecasts. The study suggests the potential for GIFTS to make important contributions to the improvement of the forecast skill of convective precipitation.
A coupled mode approach to modulation instability and envelope solitons

Nonlinear media that support envelope solitons are known to exhibit modulation instability; the modulation depth of an amplitude modulated carrier increases spontaneously and it breaks up into isolated pulses. This paper presents a simple coupled mode approach that shows the transfer of power from the carrier to the sidebands, and clearly brings out the roles played by dispersion and nonlinearity. Using this approach it is shown that line acoustic waves should exhibit this instability; the growth rate of the instability is large enough that an experimental demonstration seems feasible.
Temperature dependence of the force sensitivity of silicon cantilevers

The resonance frequency $\ensuremath{\omega}$ and internal friction ${Q}^{\ensuremath{-}1}$ of the first eigenmode of microfabricated silicon cantilevers are measured in the temperature range of 15\char21{}300 K. The analysis shows that variation of Young's modulus is responsible for the temperature dependence of the resonance frequency, whereas the dependence of the geometrical dimensions can be neglected. Accordingly, the data can be fitted by the Wachtman equation, yielding a Debye temperature ${\ensuremath{\Theta}}_{D}=634\mathrm{K}. $ The temperature variation of internal friction ${Q}^{\ensuremath{-}1}$ is analyzed in terms of Zener's theory of thermoelastic damping. Due to the temperature dependence of the thermal expansion coefficient $\ensuremath{\alpha},$ thermoelastic damping is expected to vanish at 20 K and 125 K. A minimum of internal friction is observed at 20 K, whereas the minimum at 125 K appears to be hidden by other dissipation effects. A maximum of internal friction at 160 K is observed, which is an activation peak due to phonon scattering by atomic-scale defects. The best force sensitivity is achieved at 20 K, where a factor of 10 is gained compared to room temperature.
Canonical WNT Signaling Activated by WNT7B Contributes to L-HBs-Mediated Sorafenib Resistance in Hepatocellular Carcinoma by Inhibiting Mitophagy

Simple Summary Hepatitis B virus (HBV) is the main cause of hepatocellular carcinoma (HCC) morbidity and mortality. Because of chemoresistance, sorafenib, the first-line systemic therapy for advanced HCC, has minimal advantages. According to recent research, HBV plays a role in sorafenib resistance. However, the mechanisms remain unknown. WNT signaling is one of the critical signal pathways connected to cancer chemoresistance. We found that WNT7B was overexpressed in HBV-associated HCC tissues. Large hepatitis B surface antigens (L-HBs) increased canonical WNT signaling in HCC cells through WNT7B/frizzled-4 (FZD4). In HCC, WNT7B increased cell proliferation and metastasis. By decreasing mitophagy, L-HBs produced sorafenib resistance via WNT7B. The findings suggest a potential molecular target for HBV-related HCC development and chemoresistance. Abstract Hepatocellular carcinoma (HCC) is the third leading cause of cancer death globally, with hepatitis B virus (HBV) infection accounting for over half of all cases. HBV leads to the development of HCC according to a body of literature. Our previous research and other studies also suggest that HBV causes chemotherapeutic treatment resistance, however, the mechanism is uncertain. The WNT family, which encodes secreted signaling molecules, has been linked to carcinogenesis in a variety of malignancies, including HCC. However, little is known regarding WNT7B, a WNT ligand, in the development of HCC and HBV-induced chemoresistance. In this study, the bioinformatics analysis and immunohistochemistry (IHC) staining of clinical samples revealed that WNT7B was overexpressed in HBV-associated HCC tissues versus nontumor liver tissues, which was related to HCC patient survival. Further study in vitro showed that WNT7B and its receptor frizzled-4 (FZD4) were upregulated in response to large hepatitis B surface antigens (L-HBs). L-HBs increased canonical WNT signaling in HCC cells through WNT7B/FZD4. According to functional experiments, WNT7B enhanced the cell proliferation and metastasis in HCC. In vivo and in vitro studies investigated whether L-HBs induced sorafenib resistance by WNT7B in HCC. Interestingly, L-HBs suppressed sorafenib-induced mitophagy by increasing WNT7B/CTNNB1 signaling, resulting in chemoresistance. The findings revealed that WNT7B could be a promising molecular therapeutic target as well as a predictor of sorafenib resistance in HBV-related HCC. The suppression of HBV structural proteins such as L-HBs may play a crucial role in systemic chemotherapy resistance in HBV-associated HCC.
Robust multi-stage approach for the detection of moving target from infrared imagery

We present a multi-stage classification approach to detect targets in widely varying thermal imagery. A multi-level spatial-temporal median filter is utilized to extract the background frame, with which the background clutters are suppressed by using the principal component analysis technique. A spatially related fuzzy adaptive resonance theory (ART) neural network is then applied to identify the local regions-of-interest. Within each region, another fuzzy ART neural network is utilized to detect the targets. Experimental results demonstrate that the proposed approach is capable of detecting infrared moving targets effectively for F1 measurement up to 96.3%.
A survey on grading format of automated grading tools for programming assignments

The prevalence of online platforms and studies has generated the demand for automated grading tools, and as a result, there are plenty in the market. Such tools are developed to grade coding assignments quickly, accurately, and effortlessly. Since there are varieties of tools available to cater to the diverse options of programming languages and concepts, it is overwhelming for any instructor to decide which one suits his/her’s requirements. There are several surveys studying the tools and giving insights into how they function and what they support. However other than knowing the functionality, it is important for an instructor to know how the assignments are graded and what is the format of the test cases. This is crucial since the instructor has to design the grading format and therefore requires a learning curve. This survey studies and evaluates the automated grading tools based on their evaluation format. This in turn helps a reader in deciding which tool to choose and provides an insight into what are the assessment settings and approaches used in grading the coding assignment in any specific grading tool.
An 8b9b 77.44-Gb/s Noise-Immune Spatial-Delta Coded Transceiver for Short-Reach Memory Interfaces in 28-nm CMOS

A noise-immune spatial-delta coding (SDC) scheme is proposed for single-ended multi-lane links. The SDC technique allows differential sensing of single-ended PAM2 signals for high signal integrity while still achieving the same pin efficiency as the 8b9b data bus (DBI) scheme, providing high compatibility with conventional DDR interfaces. The SDC encoding/decoding functions are implemented with simple XOR gates to minimize power and latency overhead. Continuous-time linear equalizers in the receiver compensate for distortions in incoming pseudo-differential signals with high tolerance on dynamic common-mode switching associated with the SDC operation. An 8b9b SDC transceiver prototype array composed of nine data channels and a differential clock channel has been fabricated in 28-nm CMOS technology for demonstration. The transceiver array achieves a 77.44 Gb/s aggregate data rate with 9 wires at 9.68 Gbaud/s. The bit error rate is measured to be less than 1e-12 while consuming 4.9 pJ/b from a 1.25-V supply.
Decision Analysis of Advertising and Price for Bilateral Competing Supply Chain

The outcome of centralized equilibrium, prisoner's dilemma equilibrium, and decentralized equilibrium under different decision models has been provided with regards to bilateral competing supply chain system, either side of which is composed of one manufacturer and one retailer. Theoretical analysis indicates a positive correlation between price and one's own advertising investment level and a negative correlation between price and the opponent's advertising investment level. Through analysis of numerical examples, the results reveal a first mover advantage that leads to prisoner's dilemma in the system as well as the impact that price and advertising competition intensity has on the supply chain's choice of decision model.
Catchment‐scale applications of hydraulic habitat models: Climate change effects on fish

Approaches available for estimating the ecological impacts of climate change on aquatic communities in river networks range from detailed mechanistic models applicable locally to correlative approaches applicable globally. Among them, hydraulic habitat models (HABMs) link hydraulic models of streams with biological models that reflect how organisms select microhabitat hydraulics. Coarser but more general species distribution models (SDMs) predict changes in geographic distributions; they generally involve coarse predictors such as air temperature or distance to source but neglect proximate habitat descriptors such as microhabitat hydraulics. We propose an original application of HABM for predicting the ecological impacts of climate change at large scales, a comparison of their predictions with those of SDM and a linkage of the two modelling approaches. We showcase our approach in a large catchment (Rhône River) where an available distributed hydrological model estimates present and future unregulated daily flows over the whole river network. Despite large local uncertainties, simulations showed that climate change may strongly reduce low flow percentiles (e.g., a median reduction of 38.6% for a pessimistic climate scenario), inducing important alteration of fish hydraulic habitat suitability (e.g., a median loss of 3.9%–18.7% for three modelled fish species with contrasting habitat use: brown trout, barbel and sculpin). The HABM and SDM individually predicted consistent or opposite fish responses to climate change, depending on the species and their habitat requirements. Our results illustrate that accounting for ecological responses to proximate habitat variables such as hydraulics can strongly modify projections related to climate change.