Miracle-dz/UniFAR-FTUs huggingface dataset:
N‐degron specificity of chloroplast ClpS1 in plants

The prokaryotic N‐degron pathway depends on the Clp chaperone‐protease system and the ClpS adaptor for recognition of N‐degron bearing substrates. Plant chloroplasts contain a diversified Clp protease, including the ClpS homolog ClpS1. Several candidate ClpS1 substrates have been identified, but the N‐degron specificity is unclear. Here, we employed in vitro ClpS1 affinity assays using eight N‐degron green fluorescence protein reporters containing either F, Y, L, W, I, or R in the N‐terminal position. This demonstrated that ClpS1 has a restricted N‐degron specificity, recognizing proteins bearing an N‐terminal F or W, only weakly recognizing L, but not recognizing Y or I. This affinity is dependent on two conserved residues in the ClpS1 binding pocket and is sensitive to FR dipeptide competition, suggesting a unique chloroplast N‐degron pathway.
A non-natural nucleotide uses a specific pocket to selectively inhibit telomerase activity

Telomerase, a unique reverse transcriptase that specifically extends the ends of linear chromosomes, is up-regulated in the vast majority of cancer cells. Here, we show that an indole nucleotide analog, 5-methylcarboxyl-indolyl-2′-deoxyriboside 5′-triphosphate (5-MeCITP), functions as an inhibitor of telomerase activity. The crystal structure of 5-MeCITP bound to the Tribolium castaneum telomerase reverse transcriptase reveals an atypical interaction, in which the nucleobase is flipped in the active site. In this orientation, the methoxy group of 5-MeCITP extends out of the canonical active site to interact with a telomerase-specific hydrophobic pocket formed by motifs 1 and 2 in the fingers domain and T-motif in the RNA-binding domain of the telomerase reverse transcriptase. In vitro data show that 5-MeCITP inhibits telomerase with a similar potency as the clinically administered nucleoside analog reverse transcriptase inhibitor azidothymidine (AZT). In addition, cell-based studies show that treatment with the cell-permeable nucleoside counterpart of 5-MeCITP leads to telomere shortening in telomerase-positive cancer cells, while resulting in significantly lower cytotoxic effects in telomerase-negative cell lines when compared with AZT treatment.
Suggested modifications in oncology/hematology inpatient service in Saudi Arabia during coronavirus disease-2019 (COVID-19) pandemic

Abstract Background: Management of cancer patients in the current era of coronavirus disease-2019 (COVID-19) pandemic poses significant challenges on health-care systems. However, it is mandatory to keep the required level of care of cancer patients while taking the necessary precautions to maintain the safety of both patients and health-care professionals (HCPs). The present survey explores suggested modifications of inpatient oncology/hematology care during the COVID-19 pandemic. Materials and Methods: A web-based questionnaire using SurveyMonkey was distributed to HCPs taking care of inpatient hematology/oncology service including oncologists, hematologists, and inpatient nurses in Saudi Arabia. The 25 items selected for the survey focused on five domains including characteristics of HCPs, COVID-19 infection risk among admitted patients, possible modifications related to physicians/nursing practice, and suggested infection control measures. Clinical sensibility assessment was conducted to evaluate the comprehensiveness, clarity, and face validity of our instrument on a scale of 1–5. The percentages of HCP responses to the suggested modifications in the survey were assessed in descriptive statistics to summarize data and report views of participants. Results: Of 215 HCPs, 195 responded and completed the survey. Of the respondents, 30.4% were medical oncologists, whereas hematologists and nurses constituted 6.7% and 62.9% of the participants, respectively. The majority of respondents (87.6%) work in governmental hospitals. The majority of participants (82%) have diagnosed patients with COVID-19 in their hospitals and modifications in inpatient practice during the COVID-19 pandemic were supported by 95% of respondents. The supported modifications by participants include enhanced use of oral medications (83.5%), phone calls to admitted stable patients by physicians, instead of physical interview (77%), decreasing frequency of vital signs assessment in stable patients (91%), decreasing the duration of stay in patients rooms (89%), using peripheral instead of central lines (76%), using video-based educational materials to patients through hospital TV network (91%), testing for COVID -19 before scheduled radiology imaging and procedures (74%), and performing routine nasopharyngeal swabs for HCPs (67%). Conclusion: Several modifications in inpatient oncology/hematology practice were supported by the survey participants. These suggestions need to be discussed on local basis considering local infrastructure, available resources, and level of required care.
Global 3D Non-Rigid Registration of Deformable Objects Using a Single RGB-D Camera

We present a novel global non-rigid registration method for dynamic 3D objects. Our method allows objects to undergo large non-rigid deformations and achieves high-quality results even with substantial pose change or camera motion between views. In addition, our method does not require a template prior and uses less raw data than tracking-based methods since only a sparse set of scans is needed. We simultaneously compute the deformations of all the scans by optimizing a global alignment problem to avoid the well-known loop closure problem and use an as-rigid-as-possible constraint to eliminate the shrinkage problem of the deformed shapes, especially near open boundaries of scans. To cope with large-scale problems, we design a coarse-to-fine multi-resolution scheme, which also avoids the optimization being trapped into local minima. The proposed method is evaluated on public datasets and real datasets captured by an RGB-D sensor. The experimental results demonstrate that the proposed method obtains better results than several state-of-the-art methods.
Import Tax Evasion in Cross-Border E-commerce

Cross-border e-commerce is increasingly important today. Unfortunately, this sector involves widespread under-declaration of goods' valuation (selling price) to avoid import taxes. Customs brokers play a crucial role in this value chain by ensuring proper declarations at customs, and pay stiff penalties if the retailer is caught under-reporting value in an audit. We illuminate the incentives of import tax evasion by developing a theoretical model of an optimal contract between a customs broker (principal) and an overseas retailer (agent) who may expend resources to under-value his goods, but risks getting caught in an audit. We show that fraud is inevitable at all valuations. We further show that increasing audit accuracy lowers fraud but fails to eliminate it. Our model leads to the following policy prescriptions: (a) higher import duties lead to more fraud, and (b) penalties imposed on the broker are more effective in reducing under-reporting than those imposed on the retailer. Our results can help explain observed trends in cross-border e-commerce.
A Novel Icterometer for Hyperbilirubinemia Screening in Low-Resource Settings

In this study, we report on the diagnostic accuracy of the Bili-ruler, a novel, low-cost icterometer, to screen for hyperbilirubinemia in low-resource settings. BrightcoveDefaultPlayer10.1542/6138653324001PEDS-VA_2018-2039 Video Abstract BACKGROUND: Severe neonatal hyperbilirubinemia (>20 mg/dL) affects ∼1 million infants annually. Improved jaundice screening in low-income countries is needed to prevent bilirubin encephalopathy and mortality. METHODS: The Bili-ruler is an icterometer for the assessment of neonatal jaundice that was designed by using advanced digital color processing. A total of 790 newborns were enrolled in a validation study at Brigham and Women’s Hospital (Boston) and Sylhet Osmani Medical College Hospital (Sylhet, Bangladesh). Independent Bili-ruler measurements were made and compared with reference standard transcutaneous bilirubin (TcB) and total serum bilirubin (TSB) concentrations. RESULTS: Bili-ruler scores on the nose were correlated with TcB and TSB levels (r = 0.76 and 0.78, respectively). The Bili-ruler distinguished different clinical thresholds of hyperbilirubinemia, defined by TcB, with high sensitivity and specificity (score ≥3.5: 90.1% [95% confidence interval (CI): 84.8%–95.4%] and 85.9% [95% CI: 83.2%–88.6%], respectively, for TcB ≥13 mg/dL). The Bili-ruler also performed reasonably well compared to TSB (score ≥3.5: sensitivity 84.5% [95% CI: 79.1%–90.3%] and specificity 83.2% [95% CI: 76.1%–90.3%] for TSB ≥11 mg/dL). Areas under the receiver operating characteristic curve for identifying TcB ≥11, ≥13, and ≥15 were 0.92, 0.93, and 0.94, respectively, and 0.90, 0.87, and 0.86 for identifying TSB ≥11, ≥13, and ≥15. Interrater reliability was high; 97% of scores by independent readers fell within 1 score of one another (N = 88). CONCLUSIONS: The Bili-ruler is a low-cost, noninvasive tool with high diagnostic accuracy for neonatal jaundice screening. This device may be used to improve referrals from community or peripheral health centers to higher-level facilities with capacity for bilirubin testing and/or phototherapy.
State-dependent Gaussian kernel-based power spectrum modification for accurate instantaneous heart rate estimation

Accurate estimation of the instantaneous heart rate (HR) using a reflectance-type photoplethysmography (PPG) sensor is challenging because the dominant frequency observed in the PPG signal corrupted by motion artifacts (MAs) does not usually overlap the true HR, especially during high-intensity exercise. Recent studies have proposed various MA cancellation and HR estimation algorithms that use simultaneously measured acceleration signals as noise references for accurate HR estimation. These algorithms provide accurate results with a mean absolute error (MAE) of approximately 2 beats per minute (bpm). However, some of their results deviate significantly from the true HRs by more than 5 bpm. To overcome this problem, the present study modifies the power spectrum of the PPG signal by emphasizing the power of the frequency corresponding to the true HR. The modified power spectrum is obtained using a Gaussian kernel function and a previous estimate of the instantaneous HR. Because the modification is effective only when the previous estimate is accurate, a recently reported finite state machine framework is used for real-time validation of each instantaneous HR result. The power spectrum of the PPG signal is modified only when the previous estimate is validated. Finally, the proposed algorithm is verified by rigorous comparison of its results with those of existing algorithms using the ISPC dataset (n = 23). Compared to the method without MA cancellation, the proposed algorithm decreases the MAE value significantly from 6.73 bpm to 1.20 bpm (p < 0.001). Furthermore, the resultant MAE value is lower than that obtained by any other state-of-the-art method. Significant reduction (from 10.89 bpm to 2.14 bpm, p < 0.001) is also shown in a separate experiment with 24 subjects.
Improving Speller BCI performance using a cluster-based under-sampling method

A Brain-Computer Interface (BCI) allows its user to interact with a computer or other machines by only using their brain activity. People with motor disabilities are potential users of this technology since it could allow them to interact with their surroundings without using their peripheral nerves, helping them regain their lost autonomy. The P300 Speller is one of the most popular BCI applications. Its performance depends on its classifier’s capacity to identify and discriminate the presence of the P300 potentials from electroencephalographic (EEG) signals. For the classifier to do this correctly, it is necessary to train it with a balanced data-set. However, as the P300 is usually elicited with an oddball paradigm, only unbalanced distributions can be obtained. This paper applies an under-sampling method based on Self-Organizing Maps (SOMs) on P300 EEG signals looking to increase the classifier’s accuracy. Two classifying models, a deep feedforward network (DFN) and a deep belief network (DBN), are tested with data-sets obtained from healthy subjects and post-stroke victims. We compared the results with our previous works and observed an increase of 7% in classification accuracy for our most critical subject. The DBN achieved a maximum classification accuracy of 95.53% and 94.93% for a healthy and post-stroke subject, while the DFN, 96.25% and 93.75%.
Genome-wide Identification of Powdery Mildew Resistance in Common Bean

Background: Genome-wide association studies (GWAS) have been utilized to detect genetic variations related to the powdery mildew (PM) resistance and several agronomic traits in common bean. However, its application in common bean and the PM interactions to identify genes and their location in the common bean genome has not been fully addressed.Results: Genome-wide association studies (GWAS) through marker-trait association are useful molecular tools for the identification of disease resistance and other agronomic traits. SNP genotyping with a BeadChip containing 5398 SNPs was used to detect genetic variations related to resistance to PM disease in a panel of 211 genotypes grown under field conditions for two consecutive years. Significant SNPs identified on chromosomes Pv04 and Pv10 were repeatable, confirming the reliability of the phenotypic data scored from the genotypes grown in two locations within two years. A cluster of resistance genes was revealed on the Pv04 of common bean genome among which CNL and TNL like resistance genes were identified. Furthermore, two resistance genes Phavu_010G1320001g and Phavu_010G136800g were also identified on Pv10; further sequence analysis showed that these genes were homologs to the Arabidopsis disease resistance protein (RLM1A-like) and the putative disease resistance protein (At4g11170.1), respectively. Two LRR receptor-like kinases (RLK) were also identified on Pv11 in samples collected in 2018 only. Many genes encoding auxin-responsive protein, TIFY10A protein, growth-regulating factor 5-like, ubiquitin-like protein, cell wall protein RBR3-like protein related to PM resistance were identified nearby significant SNPs. These results suggested that the resistance to PM pathogen involves a network of many genes constitutively co-expressed and may generate several layers of defense barriers or inducible reactions.Conclusion: Our results provide new insights into common bean and PM interactions, and revealed putative resistance genes as well as their location on common bean genome that could be used for marker-assisted selection, functional genomic study approaches to confirm the role of these putative genes; hence, developing common bean resistance lines to the PM disease.
Estimating uncertainty in predicted folding free energy changes of RNA secondary structures

Nearest neighbor parameters for estimating the folding stability of RNA are commonly used in secondary structure prediction, for generating folding ensembles of structures, and for analyzing RNA function. Previously, we demonstrated that we could quantify the uncertainties in each nearest neighbor parameter by perturbing the underlying optical melting data within experimental error and rederiving the parameters, which accounts for the substantial correlations that exist between the parameters. In this contribution, we describe a method to estimate uncertainty in the estimated folding stabilities of RNA structures, accounting for correlations in the nearest neighbor parameters. This method is incorporated in the RNA structure software package.
Accounting for the 'Lost Decade' in Japan

There is no debate amongst economists that Japan performed poorly during the1990s. This can be seen in falling growth rates of GDP per capita, investment per capita and mounting problems of non performing loans and ballooning Government deficit. A lot of models have tried to come up with an explanation for the Lost Decade. However, none of them have yet been able to clearly account for the growth slump. At this point, it is necessary to revisit all possible distortions that might have caused the dismal performance during the 1990s. This would help us to correctly identify the possible problem areas and search for more specific causes of downturn of the economy in a considerably narrowed field. In this paper, I have tried to bring together the different proposed theories in a consolidated way to help isolate promising theories from not so promising ones. To do so, I applied the Business Cycle Accounting procedure developed by V V Chari, Ellen R McGrattan and Patrick Kehoe to the Japanese case. I find that efficiency wedge is important in explaining the dismal performance of the Japanese economy during the 1990s but labor wedge is not very important except for a brief span of time during 1996 to 1997. My most important result is that investment wedge played a major role in the performance of the Japanese economy during the 1990s. So, any model that tries to focus on what went wrong in Japan in 1990s would do well to focus on frictions on productivity and investment financing that might be at the root of the dismal performance of the Japanese economy.
Use of Multiple Linear Regressions to Study the Effect of Credit Management Practices on Financial Performance among Front Office Services Activity SACCOs in Nairobi County, Kenya

: Front Office Service Activities (FOSA) Saving and Credit Cooperative Societies (SACCOs) have provided an avenue to deal with poverty issues by addressing specific needs of destitute and poor people. Their performance generally relies upon the adequacy of their credit management practice on the grounds that the institution creates a large portion of their income from interest netted on extended Credits and members share contribution. Good Credit management is essential for a SACCOs' stability and continued profitability but credit delinquency is the reason for poor financial performance. The main objective of this research was to investigate the effect of credit management practices on financial performance among FOSA SACCOs in Nairobi county using multiple linear regression. The credit management practices investigated in this study included; credit appraisal practice, credit risk control practice, credit recovery practice and credit rationing practice. The research employed questionnaires administered to branch managers, credit manager and Finance managers in 37 FOSA SACCOS in Nairobi county. A total of 75 respondents were recorded in this research. The results indicated that multiple linear regression equation had a coefficient of determination (R 2 ) of 0.537, with all the four credit management practices registering positive and significant influence on financial performance of FOSA SACCOs in Nairobi. It can therefore be concluded that credit appraisal practice, credit risk control practice, credit rationing practice and credit recovery practice are critical part of credit management practices for FOSA SACCOS in Nairobi. This study recommends that there is need for FOSA SACCOs to enhance their credit management practices in a bid to improve their financial performance.
Ultra-Wideband and Odometry-Based Cooperative Relative Localization With Application to Multi-UAV Formation Control

This puts forth an infrastructure-free cooperative relative localization (RL) for unmanned aerial vehicles (UAVs) in global positioning system (GPS)-denied environments. Instead of estimating relative coordinates with vision-based methods, an onboard ultra-wideband (UWB) ranging and communication (RCM) network is adopted to both sense the inter-UAV distance and exchange information for RL estimation in 2-D spaces. Without any external infrastructures prepositioned, each agent cooperatively performs a consensus-based fusion, which fuses the obtained direct and indirect RL estimates, to generate the relative positions to its neighbors in real time despite the fact that some UAVs may not have direct range measurements to their neighbors. The proposed RL estimation is then applied to formation control. Extensive simulations and real-world flight tests corroborate the merits of the developed RL algorithm.
The Ser/Thr protein kinase PrkC imprints phenotypic memory in Bacillus anthracis spores by phosphorylating the glycolytic enzyme enolase

Bacillus anthracis is the causative agent of anthrax in humans, bovine, and other animals. B. anthracis pathogenesis requires differentiation of dormant spores into vegetative cells. The spores inherit cellular components as phenotypic memory from the parent cell, and this memory plays a critical role in facilitating the spores' revival. Because metabolism initiates at the beginning of spore germination, here we metabolically reprogrammed B. anthracis cells to understand the role of glycolytic enzymes in this process. We show that increased expression of enolase (Eno) in the sporulating mother cell decreases germination efficiency. Eno is phosphorylated by the conserved Ser/Thr protein kinase PrkC which decreases the catalytic activity of Eno. We found that phosphorylation also regulates Eno expression and localization, thereby controlling the overall spore germination process. Using MS analysis, we identified the sites of phosphorylation in Eno, and substitution(s) of selected phosphorylation sites helped establish the functional correlation between phosphorylation and Eno activity. We propose that PrkC-mediated regulation of Eno may help sporulating B. anthracis cells in adapting to nutrient deprivation. In summary, to the best of our knowledge, our study provides the first evidence that in sporulating B. anthracis, PrkC imprints phenotypic memory that facilitates the germination process.
Antioxidant and Cytotoxic Effect of Water Extract of Ananas comosus in Human Breast Cancer Cell Line

Background: Breast cancer is the most common type of cancer and the second leading cause of death in the world. One of the supporting therapeutic efforts to overcome cancer is through food, mainly fruits. Ananas comosus has been investigated for its potential as an anti-cancer. It is a source of antioxidants from the content of Vitamin C and flavonoids that work by capturing free radicals, resulting in inhibition of cancer cell proliferation.Objective :This study was conducted to determine the antioxidant activity and cytotoxicity of water extract of Ananas comosus on T-47D breast cancer cell lines.Method: The process of extracting pineapple flesh is done using water as a solvent, then tested its antioxidant activity using DPPH and cytotoxicity using MTT assay on T-47D.Result: IC50 value for antioxidant activity was 463.369 μg / mL and the IC50 for the cytotoxicity assay was 488.003 μg / mL.Conclusion : The water extract of Ananas comosus have very weak antioxidant activity and moderate cytotoxicity properties that have potential as chemo preventive agents in T-47D breast cancer cell lines.