Miracle-dz/UniFAR-FTUs huggingface dataset:
High frequency of BRCA recurrent mutations in a consecutive series of unselected ovarian cancer patients

Abstract Hereditary predisposition to breast and ovarian cancer (HBOC) is diagnosed by molecular analysis of deleterious mutations in BRCA genes, allowing oncogenetic follow-up of patients and of their families. BRCA testing addresses only to HBOC families, using restrictive inclusion criteria based on familial history of cancer and age at diagnosis. Sporadic ovarian cancer has high incidence and mortality in Romania, with low median age of diagnosis and possibly a higher magnitude of hereditary contribution comparing to othe populations. However, sporadic ovarian cancers do not qualify for BRCA testing according to inclusion criteria, and a complete BRCA screening of all cancers is neither feasible nor recommended. Despite the large diversity of BRCA mutations worldwide, some recurrent mutations have higher frequencies in diverse populations. Precisely screening for recurrent mutations in a target population allows to rapidly identifying mutation carriers without sequencing the entire BRCA genes. In Romanian population and neighboring countries, several recurrent mutations have already been described. In a consecutive series of 50 sporadic ovarian cancer patients, not qualifying for BRCA complete testing, we screened for 9 most common BRCA mutations, by multiplex-PCR, RFLP and targeted Sanger sequencing. Our results revealed 6 different BRCA mutations in 8 unrelated patients, with a frequency of 16%, much higher than expected. We further recommend screening for the identified mutations in larger series of cancer patients. The results are highly beneficial to cancer patients, healthy relatives, and overall, considering prevention in cancer a priority, to public health system and future of oncogenetics in Romania
Synthesis of (‐)‐Aristeromycin from D‐Glucose.

(-)-Aristeromycin (l), a typical pseudo-nucleoside exhibiting various biological activities, was synthesized from D-glucose by using an intramolecular condensation process to form a nitro-cyclopentene (12) and by subsequent employment of a stereoselective Michael-type addition reaction of 6N-benzoyladenine to introduce a purine base moiety.
Analysis of Optimal Shift Schedule Derivation for Electric City Buses Equipped with Automatic Manual Transmission

Since most of the electric city buses equipped with automated manual transmission (AMT) are currently implemented with a heuristic strategy, this paper proposes a systematic extraction method to optimize and accelerate the shift schedule design process. A dynamic model of the electric city bus with a four-speed AMT is established to study the energy management strategy. Dynamic programming (DP) algorithm is adopted to explore the offline global optimal control sequence considering the shift frequency. Then the feature of optimal operating points is analyzed and a time-saving derivation methodology is discussed to construct the gear shift schedule based on the clustering algorithm. The derived control strategy is proved to be efficient, flexible and online implementable. Simulation results show that the derived strategy can improve the energy economy by 4.45% compared with the preliminary empirical gear shift schedule, which is 57.8% better than back-propagation neural networks in a determined city route.
Evaluation of Dietary Hydrolyzed Barley on Growth Performance, Nutrient Digestibility, Blood Characteristic, and Meat Quality in Finishing Pigs

A total of 144 [(Duroc × Yorkshire) × Landrace] pigs with an average initial BW of 61.8±1.04 kg were used in this 70-d growth experiment. Pigs were allotted to 4 treatments based on their initial BW using a randomized complete block design. Each treatment consisted of 9 replications (pen) with 4 pigs per pen (2 gilts and 2 barrows). Dietary treatments were: 1) V0, 0% hydrolyzed barley (HB) and 30% de-hulled barley (DB); 2) V1, 10% HB and 20% DB; 3) V2, 20% HB and 10% DB; and 4) V3, 30% HB and 0% DB. In this study, our analyzed data suggested that hydrolyzed barley increased the energy and CP concentration by 50.65% and 18%, respectively, compared with the de-hulled barley. In the feeding trail, Pigs fed the V2 and V3 treatment diet increased (P<0.05) the N digestibility compared with the V0 treatment at the end of 5 week. An increased (P<0.10) tendency was also observed on the energy and nitrogen digestibility at the end of 5 week and 10 week, respectively. Moreover, pigs fed the HB diet tend to increase (P<0.10) the average daily gain (ADG) and average daily feed intake (ADFI). The inclusion of V3 treatment decreased (P<0.05) the blood cholesterol compared with those contain DB. Dietary V3 treatment led to a higher (P<0.05) WHC than the V0 and V1 treatment. Pigs fed V2 and V3 treatment decreased (P<0.05) L* value compared with DB diet. In conclusion, the inclusion of hydrolyzed barley could improve the meat quality without any negative effect on the growth performance and nutrient digestibility, which provide a strong indication that hydrolyzed barley could be used as a good energy source for swine.
Factors Affecting Colony Size and Reproductive Success of Little Egret Egretta garzetta in the Sfax Salina, Tunisia

Abstract. The relationship between breeding site characteristics and breeding parameters of Little Egrets were investigated in the Sfax salt marshes (salina), Tunisia. Thirty colonies distributed among 14 breeding sites were monitored weekly during four breeding seasons (2004–2007). The number of breeding pairs varied among years in parallel with the number of detected colonies. Regressions were used to assess whether breeding site surface area, vegetation cover and inaccessibility to terrestrial predators affected the size and reproductive success of the colonies. Colony size was positively related to breeding site surface area and vegetation cover, while site isolation was the most important predictor of chick productivity. The results suggest that Little Egret colony size in the Sfax salina is determined by availability of nesting places, while chick productivity is controlled by accessibility of breeding sites to terrestrial predators, i.e. dogs. Given these results, an effective management action to conserve Little Egrets in Sfax would be to strategically place fences to protect large and densely-vegetated islets from these predators.
Human Parental Relatedness through Time - Detecting Runs of Homozygosity in Ancient DNA

At present day, human parental relatedness varies substantially across the globe, but little is known about the past. Here we use ancient DNA to provide new insights, leveraging that parental relatedness leaves traces in the offspring’s genome in the form of runs of homozygosity. We present a method to identify such runs in low-coverage ancient DNA data using linkage information from a reference panel of modern haplotypes. As a result, the method facilitates analysis of a much larger fraction of the global ancient DNA record than previously possible. Simulation and experiments show that this new method has power to detect runs of homozygosity longer than 4 centimorgan for ancient individuals with at least 0.3× coverage. We used this new method to analyze sequence data from 1,785 humans from the last 45,000 years. Generally, we detect very low rates of first cousin or closer unions across most ancient populations. Moreover, our results evidence a substantial impact of the adoption of agricultural lifestyles: We find a marked decay in background parental relatedness, co-occurring with or shortly after the advent of sedentary agriculture. We observe this signal, likely linked to increasing local population sizes, across several geographic regions worldwide.
SCFCdc4 ubiquitin ligase regulates synaptonemal complex formation during meiosis

During meiosis, homologous chromosomes pair to form the synaptonemal complex (SC). This study showed that SCFCdc4 ubiquitin ligase is required for and works with Pch2 AAA+ ATPase for SC assembly. Homologous chromosomes pair with each other during meiosis, culminating in the formation of the synaptonemal complex (SC), which is coupled with meiotic recombination. In this study, we showed that a meiosis-specific depletion mutant of a cullin (Cdc53) in the SCF (Skp-Cullin-F-box) ubiquitin ligase, which plays a critical role in cell cycle regulation during mitosis, is deficient in SC formation. However, the mutant is proficient in forming crossovers, indicating the uncoupling of meiotic recombination with SC formation in the mutant. Furthermore, the deletion of the PCH2 gene encoding a meiosis-specific AAA+ ATPase suppresses SC-assembly defects induced by CDC53 depletion. On the other hand, the pch2 cdc53 double mutant is defective in meiotic crossover formation, suggesting the assembly of SC with unrepaired DNA double-strand breaks. A temperature-sensitive mutant of CDC4, which encodes an F-box protein of SCF, shows meiotic defects similar to those of the CDC53-depletion mutant. These results suggest that SCFCdc4, probably SCFCdc4-dependent protein ubiquitylation, regulates and collaborates with Pch2 in SC assembly and meiotic recombination.
Lateralization of Auditory Processing of Silbo Gomero

Left-hemispheric language dominance is a well-known characteristic of the human language system. However, it has been shown that leftward language lateralization decreases dramatically when people communicate using whistles. Whistled languages present a transformation of a spoken language into whistles, facilitating communication over great distances. In order to investigate the laterality of Silbo Gomero, a form of whistled Spanish, we used a vocal and a whistled dichotic listening task in a sample of 75 healthy Spanish speakers. Both individuals that were able to whistle and to understand Silbo Gomero and a non-whistling control group showed a clear right-ear advantage for vocal dichotic listening. For whistled dichotic listening, the control group did not show any hemispheric asymmetries. In contrast, the whistlers’ group showed a right-ear advantage for whistled stimuli. This right-ear advantage was, however, smaller compared to the right-ear advantage found for vocal dichotic listening. In line with a previous study on language lateralization of whistled Turkish, these findings suggest that whistled language processing is associated with a decrease in left and a relative increase in right hemispheric processing. This shows that bihemispheric processing of whistled language stimuli occurs independent of language.
Analysis of Cataract in Relationship to Occupational Radiation Dose Accounting for Dosimetric Uncertainties in a Cohort of U.S. Radiologic Technologists

Cataract is one of the major morbidities in the U.S. population and it has long been appreciated that high and acutely delivered radiation doses of 1 Gy or more can induce cataract. Some more recent studies, in particular those of the U.S. Radiologic Technologists, have suggested that cataract may be induced by much lower, chronically delivered doses of ionizing radiation. It is well recognized that dosimetric measurement error can substantially alter the shape of the radiation dose-response relationship and thus, the derived study risk estimates, and can also inflate the variance of the estimates. In the current study, we evaluate the impact of uncertainties in eye-lens absorbed doses on the estimated risk of cataract in the U.S. Radiologic Technologists' Monte Carlo Dosimetry System, using both absolute and relative risk models. Among 11,345 cases we show that the inflation in the standard error for the excess relative risk (ERR) is generally modest, at most approximately 20% of the unadjusted standard error, depending on the model used for the baseline risk. The largest adjustment results from use of relative risk models, so that the ERR/Gy and its 95% confidence intervals change from 1.085 (0.645, 1.525) to 1.085 (0.558, 1.612) after adjustment. However, the inflation in the standard error of the excess absolute risk (EAR) coefficient is generally minimal, at most approximately 0.04% of the standard error.
Kinect Controlled NAO Robot for Telerehabilitation

Abstract In this paper, we focus on the human upper limb rehabilitation scheme that utilizes the concept ofteleoperation. Teleoperation can help the therapist demonstrate different rehab exercises to a different group of people at the same time remotely. Different groups of people from a different place connected to the same network can get therapy from the same therapist at the same time using the telerehabilitation scheme. Here, we presented a humanoid robot NAO that can be operated remotely by a therapist to demonstrate the exercise to a patient. To mimic the movement demonstrated by the therapist, Kinect V2 sensor which is a markerless vision-based motion-tracking device, was used. Modified Denavit-Hartenberg (DH) convention was used for the kinematic modeling of the human upper arm. From the Kinect data, a geometric solution was developed to find a unique inverse kinematic solution of human upper-extremity. Experimental results revealed that NAO could be teleoperated successfully to instruct and demonstrate patients to perform different arm movement exercises in real-time.
Investigations on the Emergence of Larvae from the Cysts of the Potato-root Eel worm, Heterodera rostochiensis.

Immersion of cysts of Heterodera rostochiensis in potato-root diffusate results in larval emergence which may occupy up to two or three months. In a previous paper (Fenwick, 1950), the author dealt with the form of the hatching curve, and showed that any given curve was controlled by three parameters; the number of larvae finally emerging, the mean reaction time of the hatchable larvae and the standard deviation of that mean reaction time expressed in log-time units. Since it was also shown that each of these parameters was subject to considerable variation, it is obvious that maximum information and accuracy can only be obtained by continuing a hatching test until all larval emergence has ceased and plotting cumulative hatches at selected intervals of tune against log-time; in this way detailed information may be obtained regarding the parameters of the hatching curve.
Screening of ESTs from Septoria musiva (teleomorph Mycosphaerella populorum) for detection of SSR and PCR–RFLP markers

The development of an expressed sequence tag (EST) collection for the poplar pathogen Septoria musiva presented an opportunity for the development of locus-specific polymorphic markers. Five microsatellites simple sequence repeat (SSR) and six polymerase chain reaction (PCR)–restriction fragment length polymorphism (RFLP) markers were identified and tested on three S. musiva populations collected in the north-central and northeastern regions of North America. The results obtained support previously published random amplified polymorphic DNA (RAPD) data.
CORRELATIONS OF DIFFERENT STRUCTURAL AND FUNCTIONAL CHARACTERISTICS OF ARTERIAL WALL WITH TRADITIONAL CARDIOVASCULAR RISK FACTORS IN HEALTHY PEOPLE OF DIFFERENT AGE. PART 2

Detection of principal subclinical arterial wall lesions is one of the most important aspects of effective cardiovascular disease (CVD) primary prevention. Such lesions include: arterial wall thickening, increased rigidity, endothelial dysfunction development. However, the role of traditional CVD risk factors in the development of individual arterial wall lesions in CVD-free people is understudied. This is particularly so with people of older age. Aim. To study the role of traditional CVD risk factors in development of arterial wall lesions in relatively healthy individuals of different age. Material and methods. We have examined a total of 303 people aged 25-91 years, with no signs of CVD and other chronic diseases and without any regular medical treatment. Anthropometric parameters, blood pressure, fasting plasma glucose, total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides levels were detected in all the patients. Measurement of pulse wave velocity was conducted using SphygmoCor device (AtCorMedical,Australia). Carotid ultrasound to measure intima-media thickness and number of atherosclerotic plaques was conducted using linear transducer with ultra-high resolution 17-5 MHz (PHILIPS iU22, the Netherlands) in the B-mode. Endothelium-dependent vasodilation was assessed by the reactive hyperemia test. Results. Multivariate linear regression analysis has revealed fasting hyperglycemia and increased systolic blood pressure to be to a greater degree associated with arterial wall state in both age groups. According to the results of multivariate logistic regression analysis a relationship between risk factors and arterial wall parameters is stronger in the younger group as compared with the older one. Conclusion. Systolic blood pressure and fasting hyperglycemia must be the main targets of CVD primary prevention in older age group, while in younger age group other traditional risk factors must be taken into account as well.
Continuing to Explore the Relation between Economic and Political Factors and Government Survey Refusal Rates: 1960–2015

Abstract In the United States, government surveys’ refusal rates have been increasing at an alarming rate, despite traditional measures for mitigating nonresponse. Given this phenomenon, now is a good time to revisit the work of Harris-Kojetin and Tucker (1999). In that study, the authors explored the relation between economic and political conditions on Current Population Survey (CPS) refusal rates over the period 1960–1988. They found evidence that economic and political factors are associated with survey refusals and acknowledged the need to extend this work as more data became available. In this study, our aim was to continue their analysis. First, we replicated their findings. Next, we ran the assumed underlying model on an extended time-period (1960–2015). Last, since we found that the model was not an ideal fit for the extended period, we revised it using available time series and incorporating information about the CPS sample design. In the extended, refined model, presidential approval, census year, number of jobs and not-in-labor-force rate were all significant predictors of survey refusal.
Natural selection in the evolution of SARS-CoV-2 in bats, not humans, created a highly capable human pathogen

RNA viruses are proficient at switching host species, and evolving adaptations to exploit the new host’s cells efficiently. Surprisingly, SARS-CoV-2 has apparently required no significant adaptation to humans since the start of the COVID-19 pandemic, with no observed selective sweeps since genome sampling began. Here we assess the types of natural selection taking place in Sarbecoviruses in horseshoe bats versus SARS-CoV-2 evolution in humans. While there is moderate evidence of diversifying positive selection in SARS-CoV-2 in humans, it is limited to the early phase of the pandemic, and purifying selection is much weaker in SARS-CoV-2 than in related bat Sarbecoviruses. In contrast, our analysis detects significant positive episodic diversifying selection acting on the bat virus lineage SARS-CoV-2 emerged from, accompanied by an adaptive depletion in CpG composition presumed to be linked to the action of antiviral mechanisms in ancestral hosts. The closest bat virus to SARS-CoV-2, RmYN02 (sharing an ancestor ∼1976), is a recombinant with a structure that includes differential CpG content in Spike; clear evidence of coinfection and evolution in bats without involvement of other species. Collectively our results demonstrate the progenitor of SARS-CoV-2 was capable of near immediate human-human transmission as a consequence of its adaptive evolutionary history in bats, not humans.
THE COMPARISON OF 2D AND 3D DETECTORS FOR TLS DATA REGISTRATION – PRELIMINARY RESULTS

Abstract. This paper presents the analysis of possible methods of a terrestrial laser scanning (TLS) data registration using 2D/3D detectors and descriptors. The developed approach, where point clouds are processed in form of panoramic images, orthoimages and 3D data, was described. The accuracy of the registration process was preliminary verified. The two approaches were analysed and compared: the 2D SIFT (Scale-Invariant Feature Transform) detector and descriptor with the rasterized TLS data and the 3D SIFT detector with the 3D FPFH (Fast Point Feature Histograms) descriptor. The feature points were found and preliminary matched using the OpenCV and PCL (Point Cloud Library) libraries. In order to find the best point cloud representation for the registration process, both the percentage and distribution of the correctly detected and matched points were analysed. The materials consisted of the point clouds of two chambers from the Museum of King John III’s Palace in Wilanów. They were acquired using the Z+F 5006h and 5003 TLS scanners. The performed analysis showed that the lowest RMSE values were for the 2D detectors and orthoimages. However, in the case of the point number and distribution, better results were obtained for using the 3D detector.
Two Anatomists Are Better than One - Dual-Level Android Malware Detection

The openness of the Android operating system and its immense penetration into the market makes it a hot target for malware writers. This work introduces Androtomist, a novel tool capable of symmetrically applying static and dynamic analysis of applications on the Android platform. Unlike similar hybrid solutions, Androtomist capitalizes on a wealth of features stemming from static analysis along with rigorous dynamic instrumentation to dissect applications and decide if they are benign or not. The focus is on anomaly detection using machine learning, but the system is able to autonomously conduct signature-based detection as well. Furthermore, Androtomist is publicly available as open source software and can be straightforwardly installed as a web application. The application itself is dual mode, that is, fully automated for the novice user and configurable for the expert one. As a proof-of-concept, we meticulously assess the detection accuracy of Androtomist against three different popular malware datasets and a handful of machine learning classifiers. We particularly concentrate on the classification performance achieved when the results of static analysis are combined with dynamic instrumentation vis-à-vis static analysis only. Our study also introduces an ensemble approach by averaging the output of all base classification models per malware instance separately, and provides a deeper insight on the most influencing features regarding the classification process. Depending on the employed dataset, for hybrid analysis, we report notably promising to excellent results in terms of the accuracy, F1, and AUC metrics.
The fluid mechanics of poohsticks

The year 2019 marked the bicentenary of George Gabriel Stokes, who in 1851 described the drag—Stokes drag—on a body moving immersed in a fluid, and 2020 is the centenary of Christopher Robin Milne, for whom the game of poohsticks was invented; his father A. A. Milne’s The House at Pooh Corner, in which it was first described in print, appeared in 1928. So this is an apt moment to review the state of the art of the fluid mechanics of a solid body in a complex fluid flow, and one floating at the interface between two fluids in motion. Poohsticks pertains to the latter category, when the two fluids are water and air. This article is part of the theme issue ‘Stokes at 200 (part 2)’.