Miracle-dz/UniFAR-FTUs huggingface dataset:
CloneQC: lightweight sequence verification for synthetic biology

Synthetic biology projects aim to produce physical DNA that matches a designed target sequence. Chemically synthesized oligomers are generally used as the starting point for building larger and larger sequences. Due to the error rate of chemical synthesis, these oligomers can have many differences from the target sequence. As oligomers are joined together to make larger and larger synthetic intermediates, it becomes essential to perform quality control to eliminate intermediates with errors and retain only those DNA molecules that are error free with respect to the target. This step is often performed by transforming bacteria with synthetic DNA and sequencing colonies until a clone with a perfect sequence is identified. Here we present CloneQC, a lightweight software pipeline available as a free web server and as source code that performs quality control on sequenced clones. Input to the server is a list of desired sequences and forward and reverse reads for each clone. The server generates summary statistics (error rates and success rates target-by-target) and a detailed report of perfect clones. This software will be useful to laboratories conducting in-house DNA synthesis and is available at http://cloneqc.thruhere. net/ and as Berkeley Software Distribution (BSD) licensed source.
Midostaurin: A New Oral Agent Targeting FMS‐Like Tyrosine Kinase 3‐Mutant Acute Myeloid Leukemia

Acute myeloid leukemia (AML), a clonal hematologic malignancy that results in bone marrow failure, is the most common acute leukemia in adults (median age of diagnosis 67 yrs), and treatment options, especially in the elderly population, are limited. Induction chemotherapy with 7 + 3, the combination of continuous‐infusion cytarabine and intermittent dosing of an anthracycline administered over 7 and 3 days, respectively, has remained the standard of care since its introduction in 1973 in the United States. Midostaurin is a first‐generation FMS‐like tyrosine kinase 3 (FLT3) inhibitor (TKI) that was approved by the U.S. Food and Drug Administration in April 2017 for the treatment of FLT3‐mutant AML. We performed a search of the PubMed database (January 1990–January 2017) to review pertinent clinical trials of midostaurin. Phase I, II, and III trials reported in English evaluating the safety and efficacy of midostaurin in patients with AML or myelodysplastic syndrome were included. The ClinicalTrials.gov database was also searched for ongoing trials. In the only phase III trial that has been conducted to date, midostaurin demonstrated significant improvement compared with placebo in overall and event‐free survival in patients aged 18–59 years with newly diagnosed FLT3‐mutant AML treated with standard induction chemotherapy. The median overall survival for patients randomized to the midostaurin group was 74.7 months versus 25.6 months in the placebo group (hazard ratio [HR] 0.78, 95% confidence interval [CI] 0.63–0.96, p=0.009). Median event‐free survival was 8.2 months with midostaurin compared with 3.0 months with placebo (HR 0.78, 95% CI 0.66–0.93, p=0.002). In addition to being evaluated in combination with conventional chemotherapy, midostaurin has been studied as monotherapy, in combination with the hypomethylating agents azacitidine and decitabine, and as single‐agent maintenance. Studies evaluating midostaurin in the maintenance setting after allogeneic stem cell transplantation are underway. Midostaurin is the first oral multitargeted TKI to improve overall survival in patients with FLT3‐mutant AML and represents an important addition to the limited armamentarium against AML.
Epigenetic Gene Promoter Methylation at Birth Is Associated With Child’s Later Adiposity

OBJECTIVE Fixed genomic variation explains only a small proportion of the risk of adiposity. In animal models, maternal diet alters offspring body composition, accompanied by epigenetic changes in metabolic control genes. Little is known about whether such processes operate in humans. RESEARCH DESIGN AND METHODS Using Sequenom MassARRAY we measured the methylation status of 68 CpGs 5′ from five candidate genes in umbilical cord tissue DNA from healthy neonates. Methylation varied greatly at particular CpGs: for 31 CpGs with median methylation ≥5% and a 5–95% range ≥10%, we related methylation status to maternal pregnancy diet and to child’s adiposity at age 9 years. Replication was sought in a second independent cohort. RESULTS In cohort 1, retinoid X receptor-α (RXRA) chr9:136355885+ and endothelial nitric oxide synthase (eNOS) chr7:150315553+ methylation had independent associations with sex-adjusted childhood fat mass (exponentiated regression coefficient [β] 17% per SD change in methylation [95% CI 4–31], P = 0.009, n = 64, and β = 20% [9–32], P < 0.001, n = 66, respectively) and %fat mass (β = 10% [1–19], P = 0.023, n = 64 and β =12% [4–20], P = 0.002, n = 66, respectively). Regression analyses including sex and neonatal epigenetic marks explained >25% of the variance in childhood adiposity. Higher methylation of RXRA chr9:136355885+, but not of eNOS chr7:150315553+, was associated with lower maternal carbohydrate intake in early pregnancy, previously linked with higher neonatal adiposity in this population. In cohort 2, cord eNOS chr7:150315553+ methylation showed no association with adiposity, but RXRA chr9:136355885+ methylation showed similar associations with fat mass and %fat mass (β = 6% [2–10] and β = 4% [1–7], respectively, both P = 0.002, n = 239). CONCLUSIONS Our findings suggest a substantial component of metabolic disease risk has a prenatal developmental basis. Perinatal epigenetic analysis may have utility in identifying individual vulnerability to later obesity and metabolic disease.
Changes in hemodynamics of the carotid and middle cerebral arteries before and after endoscopic sympathectomy in patients with palmar hyperhidrosis: preliminary results.

OBJECT The purpose of this study was to analyze the change in carotid and middle cerebral artery (MCA) hemodynamics before and after endoscopic upper thoracic sympathectomy in patients with palmar hyperhidrosis (PH). METHODS Sixty-eight patients with PH (35 males and 33 females) for whom the average age was 24.5+/-10.7 years (+/- standard deviation) were recruited into this study. These patients all underwent routine upper T-2 sympathectomy to treat their PH. Ultrasonography studies of the carotid arteries (CAs) and MCA were obtained in each patient before and after T-2 sympathectomy. The blood flow volume, flow velocity, and resistivity index (RI) in the bilateral common CAs (CCAs), internal CAs (ICAs), and external CAs (ECAs) were evaluated using duplex ultrasonography. The systolic peak velocity, mean velocity, diastolic peak velocity, pulsatility index, and RI of the bilateral MCAs were evaluated using transcranial Doppler ultrasonography. Blood pressure and heart rate were also recorded during this study. The Student paired t-test was used to analyze the differences between studies before and after bilateral T-2 sympathectomy. There was a significant reduction in diastolic pressure after T-2 sympathectomy (p = 0.003), but not in systolic pressure or heart rate. The vessel diameter was increased after sympathectomy in the left CAs and right CCA. The T-2 sympathectomy led to significant elevation of blood flow volume and RI in the left CCA, ICA, and ECA (p < 0.05). The authors found significant increases in maximum flow velocity and RI in the left MCA (p < 0.05). CONCLUSIONS Patients who underwent T-2 sympathectomy demonstrated a significant increase in blood flow volume and flow velocities of the CAs and MCA, especially on the left side. Asymmetry of sympathetic influence on the hemodynamics of the CAs and MCA was noted. The usefulness of sympathectomy for the treatment of ischemic cardiovascular and cerebrovascular disease deserves further investigation.
Juicios de infidelidad: un estudio exploratorio de sus determinantes

El objetivo de este estudio consiste en contribuir para una mejor comprension de los determinantes de los juicios acerca de la existencia de infidelidad marital y su gravedad, sobre los cuales existe poca investigacion a pesar de su impacto en las relaciones de pareja. Una muestra de 68 hombres y 221 mujeres respondieron online a un cuestionario en el cual se preguntaba si lo sucedido en un conjunto de escenarios constituiria infidelidad y cual seria su gravedad. Un analisis factorial identifico cuatro aspectos que determinan la evaluacion de la infidelidad: envolvimiento afectivo, contacto fisico/sexual, comportamiento inocente y consentimiento por parte de la pareja. Se atribuye mayor gravedad cuando el envolvimiento es deliberado, continuado y sexual. Adultos jovenes y ancianos, personas mas religiosas y con posicionamiento politico mas conservador realizan juicios mas severos. Las mujeres penalizan mas el envolvimiento a traves de internet. La pasion y el consentimiento de la pareja atenuan la gravedad. Situaciones ambiguas son juzgadas como mas graves por la pareja que por el propio autor/a del comportamiento.
Fault detection capabilities of coupling-based OO testing

Object-oriented programs cause a shift in focus from software units to the way software classes and components are connected. Thus, we are finding that we need less emphasis on unit testing and more on integration testing. The compositional relationships of inheritance and aggregation, especially when combined with polymorphism, introduce new kinds of integration faults, which can be covered using testing criteria that take the effects of inheritance and polymorphism into account. This paper demonstrates, via a set of experiments, the relative effectiveness of several coupling-based OO testing criteria and branch coverage. OO criteria are all more effective at detecting faults due to the use of inheritance and polymorphism than branch coverage.
Musculoskeletal quadruped robot with Torque-Angle Relationship Control System

Systems with changeable mechanical properties show promise for expanding the applications of dynamic robots. We proposed the Torque-Angle Relationship Control System (TARCS) for musculoskeletal robots with changeable output properties. First, we formulated TARCS and examined its static properties. Next, we used TARCS to change the properties and investigated the effect of the same on the jumping ability through simulations. We found that TARCS in a biarticular muscle determined the general shape of the jumpable range. Furthermore, TARCS in a monoarticular muscle could change the amplitude of the jumpable range. Both TARCS also changed the directional property of the reaction to the disturbance. Finally, we developed a musculoskeletal quadruped robot in which TARCS was implemented. This robot could change its jumping direction using TARCS, and it jumped to a height of 0.254 m at the lowest point of its body.
GCC-Plugin for Automated Accelerator Generation and Integration on Hybrid FPGA-SoCs

In recent years, architectures combining a reconfigurable fabric and a general purpose processor on a single chip became increasingly popular. Such hybrid architectures allow extending embedded software with application specific hardware accelerators to improve performance and/or energy efficiency. Aiding system designers and programmers at handling the complexity of the required process of hardware/software (HW/SW) partitioning is an important issue. Current methods are often restricted, either to bare-metal systems, to subsets of mainstream programming languages, or require special coding guidelines, e.g., via annotations. These restrictions still represent a high entry barrier for the wider community of programmers that new hybrid architectures are intended for. In this paper we revisit HW/SW partitioning and present a seamless programming flow for unrestricted, legacy C code. It consists of a retargetable GCC plugin that automatically identifies code sections for hardware acceleration and generates code accordingly. The proposed workflow was evaluated on the Xilinx Zynq platform using unmodified code from an embedded benchmark suite.
A Context-Dependent Sentiment Analysis of Online Product Reviews based on Dependency Relationships

Consumers often view online consumer product review as a main channel for obtaining product quality information. Existing studies on product review sentiment analysis usually focus on identifying sentiments of individual reviews as a whole, which may not be effective and helpful for consumers when purchase decisions depend on specific features of products. This study proposes a new feature-level sentiment analysis approach for online product reviews. The proposed method uses an extended PageRank algorithm to extract product features and construct expandable context-dependent sentiment lexicons. Moreover, consumers’ sentiment inclinations toward product features expressed in each review can be derived based on term dependency relationships. The empirical evaluation using consumer reviews of two different products shows a higher level of effectiveness of the proposed method for sentiment
Associative learning in the dengue vector mosquito, Aedes aegypti: avoidance of a previously attractive odor or surface color that is paired with an aversive stimulus

SUMMARY Associative learning has been shown in a variety of insects, including the mosquitoes Culex quinquefasciatus and Anopheles gambiae. This study demonstrates associative learning for the first time in Aedes aegypti, an important vector of dengue, yellow fever and chikungunya viruses. This species prefers to rest on dark surfaces and is attracted to the odor of 1-octen-3-ol. After training in which a dark surface alone or a dark surface with odor was paired with electric shock, mosquitoes avoided the previously attractive area. The association was stronger when odor was included in training, was retained for at least 60 min but not for 24 h, and was equal for males and females. These results demonstrate the utility of a bulk-training paradigm for mosquitoes similar to that used with Drosophila melanogaster.
Interference Mitigation in GNSS Receivers by a Time-Frequency Approach

Undesired interfering signals are considered to be one of the main threats to the correct behavior of new Global Navigation Satellite System (GNSS) receivers. There is a huge variety of interference that can occur in the real world, such as narrow band, wide band, impulsive, stationary, or nonstationary CWs. Processing techniques based on time-frequency (TF) distributions allow one to detect and mitigate many different types of these undesired signals. A TF mitigation technique is proposed to enable GNSS receivers to reduce the interference affecting the incoming signal. The proposed algorithm uses a synthesis technique based on the orthogonal-like Gabor expansion, in order to obtain an estimate of the interference, that is then subtracted from the input signal. In the presence of a wide class of deterministic interfering signals, the proposed mitigation strategy is effective in terms of acquisition and tracking performance and outperforms other algorithms described in the literature.
Cognition is the Key to the Next Generation of Radar Systems

Motivated by the echo-location system of a bat, I described the idea of cognitive radar in 2006 for the first time. This paper expands on this novel idea. In particular, the paper focuses on a cognitive tracking radar, the implementation of which comprises two distinct functional blocks, one in the receiver and the other in transmitter with a feedback link from the receiver to the transmitter. To sense the radar environment, the receiver uses approximate Bayesian filtering, which is closely realized by a new nonlinear sequential state estimator, named the Cubature Kalman filter. To control the radar illumination, the transmitter uses an incremental dynamic programming, known as the Q-learning algorithm.
Warranty forecasting of electronic boards using short-term field data

The main goal of our study is precisely predicting the reliability performance of electronic boards throughout the warranty period by using short-term field return data. We have cooperated with one of the Europe's largest manufacturers and use their well-maintained data with over 1000 electronic board failures. Before using the field data for our model of warranty forecasting, we filter it to eliminate improper data, correlated to incomplete and poorly collected data. Our model is based on a two-parameter Weibull distribution, chosen from many other distribution options regarding optimum curve fitting. In the fitting process we use and compare “Bayesian”, “rank regression”, and “maximum likelihood” fitting techniques. Our method has two steps. In the first step, we investigate how the Weibull parameter β changes by increasing the number of months of field data. For this purpose we use an electronic board with 36 months (full warranty period) of field return data. We develop a mathematical model of β as a function of the field data time interval and board dependent parameters. In the second step, we make a warranty forecasting of a new electronic board using its 3-month field data by using the mathematical model developed in the first step. The proposed method is evaluated by applying it to different electronic boards with 36 months (full warranty period) of field return data. The predicted results from our method and the direct results from the field return data matches well. This demonstrates the accuracy of our model.
Functional neuroimaging and presenting psychiatric features in frontotemporal dementia

Background: Frontotemporal dementia (FTD) is a behavioural syndrome caused by degeneration of the frontal and anterior temporal lobes. Behavioural disturbances include psychiatric features. Whether patients with FTD present with psychiatric features varies with the initial neuroanatomical variability of FTD. Objective: To identify presenting psychiatric changes not part of diagnostic criteria of FTD and contrast them with the degree of hemispheric asymmetry and frontal and temporal hypoperfusion on single photon emission computed tomography (SPECT) imaging. Methods: 74 patients who met consensus criteria for FTD were evaluated at a two year follow up. All had brain SPECT on initial presentation. Results of an FTD psychiatric checklist were contrasted with ratings of regional hypoperfusion. Results: The regions of predominant hypoperfusion did not correlate with differences on FTD demographic variables but were associated with presenting psychiatric features. Dysthymia and anxiety were associated with right temporal hypoperfusion. “Moria” or frivolous behaviour also occurred with temporal lobe changes, especially on the right. The only significant frontal lobe feature was the presence of a peculiar physical bearing in association with right frontal hypoperfusion. Conclusions: Patients with FTD may present with psychiatric changes distinct from the behavioural diagnostic criteria for this disorder. Early temporal involvement is associated with frivolous behaviour and right temporal involvement is associated with emotional disturbances. In contrast, those with right frontal disease may present with alterations in non-verbal behaviour.
If Current and Spontaneous Activity in Mouse Embryonic Ventricular Myocytes

Knowledge of the initiation of electrical and contractile activity in the embryonic heart relies to a large extent on data obtained in chicken. In recent years, molecular biological techniques have raised an interest in mouse physiology, including early embryonic development. We studied action potentials and the occurrence of one of the pacemaker currents, If, by the whole-cell voltage and current-clamp technique at the earliest stage at which a regular heartbeat is established (9.5 days postcoitum) and at 1 day before birth. We show, first, that at the early stage there is a prominent If in mouse embryonic ventricles, which decreases by 82% before birth in concert with the loss of regular spontaneous activity of ventricular cells. Second, the decrease in If current is associated with a slight change in channel gating kinetics and a decrease in total mRNA expression of the genes encoding for If current. Third, the most prevalent mRNA subtype is switched from HCN4 to HCN2 during the second half of embryonic development. Fourth, the If current may be modulated by the &bgr;-adrenergic cascade, although the coupling to the &bgr;-adrenoceptor in the sarcolemma itself is not yet mature. We conclude that If current of the sinus node type is present in early embryonic mouse ventricular cells. In association with a loss of If current, the ventricle tends to lose pacemaker potency during the second half of embryonic development.
IBWS: IST Bioinformatics Web Services

The Bioinformatics group at the National Cancer Research Institute (IST) of Genoa has been involved since many years in the development and maintenance of biomedical information systems. Among them, the Common Access to Biological Resources and Information network services offer access to more than 130 000 biological resources, like strains of micro-organisms and human and animal cell lines, included in 29 collections from some of the most known European Biological Resource Centers. An Sequence Retrieval System (SRS) implementation of the TP53 Mutation Database of the International Agency for Research on Cancer (Lyon) was made available in order to improve interoperability of this data with other molecular biology databases. ‘SRS by WS (SWS)’, a system for retrieving information on public SRS sites and for directly querying them, was also implemented. In order to make this information available through application programming interfaces, we implemented a suite of free web services (WS), called the ‘IST Bioinformatics Web Services (IBWS)’. A support web site, including a description of the system, a list of available WS together with help pages, links to corresponding WSDLs and forms for testing services, is available at http://bioinformatics.istge. it/ibws/. WSDL definitions can also be retrieved directly at http://bioinformatics.istge. it:8080/axis/services.
Protecting privacy in tabular healthcare data: explicit uncertainty for disclosure control

Summary medical data provides important statistical information for public health, but risks revealing confidential patient information. This risk is particularly difficult to assess when many different tables are released, independently protected against disclosure by various techniques. In this paper, we present a new technique for disclosure control in tabular data which uses explicit uncertainty to prevent small numbers of records from being identified disclosively. In contrast to other techniques, bounds on the cell perturbations are also made public. This technique can be applied effectively to large datasets in their entirety, automatically, and the transformed data can then be used to create the derivative tables, or hosted on a public web site. It is even safe for population-based data. Furthermore, we show that this transformation is computationally efficient while ensuring k-anonymity, and demonstrate the suitability of the transformed data for further statistical analysis.
Rendering of X3D content on mobile devices with OpenGL ES

The availability of more powerful mobile devices, sometimes equipped with graphics accelerators, is making it easier to experiment with mobile 3D graphics. In this paper, we exploit the main emerging standard in 3D rendering on mobile devices (OpenGL ES) to build a mobile player (called MobiX3D) for X3D and H-Anim content. The rendering engine of the MobiX3D player supports classic lighting and shading algorithms. We discuss the performance of the player and we apply it to sign language visualization.