Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of UHPLC high-resolution Orbitrap mass spectrometry to investigate the genes involved in the production of secondary metabolites in Aspergillus flavus

The fungus Aspergillus flavus is known for its ability to produce the toxic and carcinogenic aflatoxins in food and feed. While aflatoxins are of most concern, A. flavus is predicted to be capable of producing many more metabolites based on a study of its complete genome sequence. Some of these metabolites could be of great importance in food and feed safety. Here we describe an analytical methodology based on Orbitrap HRMS technology that allows the untargeted determination of fungal metabolites, in support of the study of the function of genes involved in secondary metabolism in fungi. The applied strategy implies the detection and identification of differentially expressed metabolites in extracts of wild-type and mutant fungal strains, using Orbitrap high-resolution mass spectrometry (HRMS) accurate mass data. The suitability of this approach was demonstrated by the confirmation of previously characterised genes involved in the aflatoxin biosynthetic pathway, namely a polyketide synthase (pksA), an oxidoreductase (ordA) and a methyltransferase (omtA) gene. Subsequently, the proposed methodology was applied for the detection and identification of metabolites produced by a yet uncharacterised gene cluster in A. favus, cluster 23. Comparative Orbitrap HRMS analysis of extracts of A. flavus wild-type strain and an over-expression mutant for the transcription factor of gene cluster 23 (lepE) demonstrated that this gene cluster is responsible for the production a set of 2-pyridone derivatives, the leporins. Besides the known derivatives leporin B and leporin B precursor that could be identified by automatic de-replication of the accurate mass data, five other compounds belonging to this class of fungal secondary metabolites were detected and identified for the first time, combining MS and multiple-stage MS data.
Co-creativity and Perceptions of Computational Agents in Co-creativity

How are computers typically perceived in co-creativity scenarios? And how does this affect how we evaluate computational creativity research systems that use co-creativity? Recent research within computational creativity considers how to attribute creativity to computational agents within co-creative scenarios. Human evaluation forms a key part of such attribution or evaluation of creative contribution. The use of human opinion to evaluate computational creativity, however, runs the risk of being distorted by conscious or subconscious bias. The case study in this paper shows people are sig-niﬁcantly less conﬁdent at evaluating the creativity of a whole co-creative system involving computational and human participants, compared to the (already tricky) task of evaluating individual creative agents in isolation. To progress co-creativity research, we should combine the use of co-creative computational models with the ﬁndings of computational creativity evaluation research into what contributes to software creativity.
KCNQ5 reaches synaptic endings in the auditory brainstem at hearing onset and targeting maintenance is activity‐dependent

Kv7.5/KCNQ5, a voltage‐dependent potassium channel that generates a subthreshold K+ current (also called M‐current), is localized in excitatory endings of auditory brainstem nuclei in the adult rat. Here, we focus on how specific targeting develops from birth to adulthood in the rat. We first analyzed by immunocytochemistry the distribution of KCNQ5 during postnatal development of neurons in the anteroventral cochlear nucleus (AVCN) and their targets in the medial nucleus of the trapezoid body (MNTB). From postnatal days (P) 0 to 12, KCNQ5 immunoreactivity was restricted to cell bodies, whereas from P13 onward a shift in labeling pattern was seen, with KCNQ5 immunoreactivity becoming confined to synaptic endings in both the AVCN and MNTB. The developmental synaptic targeting was also accompanied by a downregulation of KCNQ5 transcripts in the cochlear nucleus from P13 onward, as seen with quantitative reverse transcriptase polymerase chain reaction. We further tested whether auditory nerve activity at hearing onset (approximately P12) regulates synaptic targeting of the channel. Cochleae were removed at P10, before hearing onset. In the MNTB, 3 days after cochlear ablation, at P13, KCNQ5 immunoreactivity was seen in calyces of Held, as in normal age‐matched controls. However, immunolabeling virtually disappeared from MNTB calyces 40 days after cochlear ablation but reappeared in the somata of neurons in AVCN. These findings suggest that synaptic targeting of KCNQ5 in brainstem auditory neurons occurs around the time of hearing onset, regardless of auditory nerve activity. However, long‐term synaptic localization after hearing onset depends on peripheral input. J. Comp. Neurol. 518:1301–1314, 2010. © 2009 Wiley‐Liss, Inc.
A Visual Latency Estimator for 3D Tele-Immersion

3D Tele-Immersion systems allow geographically distributed users to interact in a virtual world using their "live" 3D models. The capture, reconstruction, transfer, and rendering of these models introduce significant latency into the system. Implicit Latency (ℒ') can be estimated using system clocks to measure the time after the data was received from the RGB-D camera, till the request to render the result. The Observed Latency (ℒ) between a real world event and the event being rendered on the display, cannot be accurately represented by ℒ' since ℒ' ignores the time taken to capture, or update the display, etc. In this paper, a Visual Pattern based Latency Estimation (VPLE) approach is introduced to calculate the real world visual latency of a system without the need for any custom hardware. VPLE generates a constantly changing pattern that is captured and rendered by the 3DTI system. An external observer records both the pattern and the rendered results at high frame rates. ℒ is estimated by calculating the difference between the generated and rendered patterns. VPLE is extended to allow ℒ estimation between geographically distributed sites. Evaluations show that the accuracy of VPLE depends on the refresh rate of the pattern, and is within 4ms. ℒ of a distributed 3DTI system implemented on the GPU is significantly lower than the CPU implementation, and is comparable to video streaming. It is also shown that the ℒ' estimates for GPU based 3DTI implementations are off by almost 100% compared to the ℒ.
Endophilin A2 Influences Volume-Regulated Chloride Current by Mediating ClC-3 Trafficking in Vascular Smooth Muscle Cells.

BACKGROUND Previous research has demonstrated that ClC-3 is responsible for volume-regulated Cl-current (ICl.vol) in vascular smooth muscle cells (VSMCs). However, it is still not clear whether and how ClC-3 is transported to cell membranes, resulting in alteration ofICl.vol.Methods and Results:Volume-regulated chloride current (ICl.vol) was recorded by whole-cell patch clamp recording, and Western blotting and co-immunoprecipitation were performed to examine protein expression and protein-protein interaction. Live cell imaging was used to observe ClC-3 transporting. The results showed that an overexpression of endophilin A2 could increaseICl.vol, while endophilin A2 knockdown decreasedICl.vol. In addition, the SH3 domain of endophilin A2 mediated its interaction with ClC-3 and promotes ClC-3 transportation from the cytoplasm to cell membranes. The regulation of ClC-3 channel activity was also verified in basilar arterial smooth muscle cells (BASMCs) isolated from endophilin A2 transgenic mice. Moreover, endophilin A2 increase VSMCs proliferation induced by endothelin-1 or hypo-osmolarity. CONCLUSIONS The present study identified endophilin A2 as a ClC-3 channel partner, which serves as a new ClC-3 trafficking insight in regulatingICl.volin VSMCs. This study provides a new mechanism by which endophilin A2 regulates ClC-3 channel activity, and sheds light on how ClC-3 is transported to cell membranes to play its critical role as a chloride channel in VSMCs function, which may be involved in cardiovascular diseases. (Circ J 2016; 80: 2397-2406).
Dihydroxyacetone Induced Autophagy in African Trypanosomes

Dihydroxyacetone (DHA) was examined to explore its trypanocidal activity. The compound is easily taken up by trypanosomes via its aquaglyceroporins but is not converted to a glycolytic intermediate due to the lack of a respective kinase. Investigating the DHA-induced cell death it became evident that parasites die by autophagy rather than by necrosis or apoptosis. Since autophagy is not well studied in African trypanosomes our work offers a way to investigate the importance of autophagy for trypanosomes not only for stress coping but also for organelle reconstruction during differentiation. Antiproliferative Effect of Dihydroxyacetone on Trypanosoma brucei Bloodstream Forms: Cell Cycle Progression, Subcellular Alterations and Cell Death N.L. Uzcátegui, D. Carmona-Gutiérrez, V. Denninger, C. Schoenfeld, F. Lang, K. Figarella and M. Duszenko Antimicrob Agents Chemother 2007; In press
Oral Contraceptive Use and Breast Cancer: A Prospective Study of Young Women

Background: Previous studies convincingly showed an increase in risk of breast cancer associated with current or recent use of oral contraceptives from the 1960s to 1980s. The relation of contemporary oral contraceptive formulations to breast cancer risk is less clear. Methods: We assessed lifetime oral contraceptive use and the specific formulations used among 116,608 female nurses ages 25 to 42 years at enrollment in 1989, and subsequently updated this information every 2 years. We related this information to risk of breast cancer up to June 1, 2001. Results: During 1,246,967 person-years of follow-up, 1,344 cases of invasive breast cancer were diagnosed. Past use of any oral contraceptive was not related to breast cancer risk [multivariate relative risk (RR), 1.12; 95% confidence interval 0.95-1.33]. Current use of any oral contraceptive was related to a marginally significant higher risk (multivariate RR, 1.33; 95% CI, 1.03-1.73). One specific formulation substantially accounted for the excess risk: the RR for current use of triphasic preparations with levonorgestrel as the progestin was 3.05 (95% CI, 2.00-4.66; P < 0.0001). Conclusions: Current use of oral contraceptives carries an excess risk of breast cancer. Levonorgestrel used in triphasic preparations may account for much of this elevation in risk. Impact: Different oral contraceptive formulations might convey different risks of breast cancer; ongoing monitoring of these associations is necessary as oral contraceptive formulations change. Cancer Epidemiol Biomarkers Prev; 19(10); 2496–502. ©2010 AACR.
Dynamic Program Behavior Identification for High Performance CMPs with Private LLCs

Chip Multi-Processors (CMPs) emerge as a mainstream architectural design alternative for high performance parallel and distributed computing. Last Level Cache (LLC) management is critical to CMPs because off-chip accesses often require a long latency. Due to its short access latency, well performance isolation and easy scalability, private cache is an attractive design alternative for LLC of CMPs. This paper proposes program Behavior Identification-based Cache Sharing (BICS) for LLC management. BICS is based on a private cache organization for the shorter access latency. Meanwhile, BICS tries to simulate a shared cache organization by allowing evicted blocks of one private LLC to be saved at peer LLCs. This technique is called spilling. BICS identifies cache behavior types of applications at runtime. When a cache block is evicted from a private LLC, cache behavior characteristics of the local application are evaluated so as to determine whether the block is to be spilled. Spilled blocks are allowed to replace some valid blocks of the peer LLCs as long as the interference is within a reasonable level. Experimental results using a full system CMP simulator show that BICS improves the overall throughput by as much as 14.5%, 12.6%, 11.0%and 11.7% (on average 8.8%, 4.8%, 4.0% and 6.8%) over private cache, shared cache, Utility-based Cache Partitioning (UCP) scheme and the baseline spilling-based organization Cooperative Caching (CC) respectively on a 4-core CMP for SPEC CPU2006 benchmarks.
Increased Autolysis of &mgr;‐Calpain in Skeletal Muscles of Chronic Alcohol‐Fed Rats

BACKGROUND Proteolysis can proceed via several distinct pathways such as the lysosomal, calcium-dependent, and ubiquitin-proteasome-dependent pathways. Calpains are the main proteases that cleave a large variety of proteins, including the giant sarcomeric proteins, titin and nebulin. Chronic ethanol feeding for 6 weeks did not affect the activities of μ-calpain and m-calpain in the m. gastrocnemius. In our research, changes in μ-calpain activity were studied in the m. gastrocnemius and m. soleus of chronically alcohol-fed rats after 6 months of alcohol intake. METHODS SDS-PAGE analysis was applied to detect changes in titin and nebulin contents. Titin phosphorylation analysis was performed using the fluorescent dye Pro-Q Diamond. Western blotting was used to determine μ-calpain autolysis as well as μ-calpain and calpastatin contents. The titin and nebulin mRNA levels were assessed by real-time PCR. RESULTS The amounts of the autolysed isoform (78 kDa) of full-length μ-calpain (80 kDa) increased in the m. gastrocnemius and m. soleus of alcohol-fed rats. The calpastatin content increased in m. gastrocnemius. Decreased intact titin-1 (T1) and increased T2-proteolytic fragment contents were found in the m. gastrocnemius and m. soleus of the alcohol-fed rats. The nebulin content decreased in the rat gastrocnemius muscle of the alcohol-fed group. The phosphorylation levels of T1 and T2 were increased in the m. gastrocnemius and m. soleus, and decreased titin and nebulin mRNA levels were observed in the m. gastrocnemius. The nebulin mRNA level was increased in the soleus muscle of the alcohol-fed rats. CONCLUSIONS In summary, our data suggest that prolonged chronic alcohol consumption for 6 months resulted in increased autolysis of μ-calpain in rat skeletal muscles. These changes were accompanied by reduced titin and nebulin contents, titin hyperphosphorylation, and development of hindlimb muscle atrophy in the alcohol-fed rats.
Stacking the Deck for Success in Interprofessional Collaboration

The practice of interprofessional collaboration is increasingly being recognized as an important skill for educators, health professionals, and social service providers. Collaboration involves team building and developing integrated service delivery mechanisms to improve outcomes for recipients of health, education, and social services. The focus on health promotion and illness prevention has led to an increasing demand for health educators to become involved in these collaboratives as members and more often as facilitators. Key concepts associated with early stages of collaborative development are described, with a focus on forming a group identity and weathering the conflicts associated with task and personnel issues. Descriptions and instructions for facilitating activities to move the group successfully through these initial stages are described.
ROS mediates baicalin-induced apoptosis in human promyelocytic leukemia HL-60 cells through the expression of the Gadd153 and mitochondrial-dependent pathway.

BACKGROUND Chemotherapy agents, particularly those that can induce apoptosis, are the major intervening strategy in the treatment of leukemia. In this study, we investigated the effects of baicalin (a compound obtained from Scutellaria baicalensis Georgi and S. rivularis Benth Labiateae) on the viability, induction of apoptosis and associated mechanism in human leukemia HL-60 cells. MATERIALS AND METHODS The cell viability and apoptosis was examined by flow cytometric analysis. The results showed that baicalin induced cytotoxicity in a dose- and time-dependent manner through the activation of caspase-3, as shown by treatment of HL-60 cells with an inhibitor of caspase-3 (z-VAD-fmk). Baicalin increased the levels of ROS, Ca2+ and decreased mitochondrial membrane potential in HL-60 cells. Western blot demonstrated that baicalin promoted the levels of Gadd153, Bax, cytochrome c and caspase-3 and -12, but decreased the levels of Grp78 and Bcl-2 in HL-60 cells. CONCLUSION Baicalin was found to induce apoptosis in HL-60 cells through multiple pathways.
Investigations on search methods for speech recognition using weighted finite-state transducers

The search problem in the statistical approach to speech recognition is to find the most likely word sequence for an observed speech signal using a combination of knowledge sources, i.e. the language model, the pronunciation model, and the acoustic models of phones. The resulting search space is enormous. Therefore, an efficient search strategy is required to compute the result with a feasible amount of time and memory. The structured statistical models as well as their combination, the search network, can be represented as weighted finite-state transducers. The combination of the individual transducers and their optimization for size and structure is achieved by means of weighted transducer algorithms. The construction of the transducer can be performed on-the-fly during the search, such that only parts of the search network are generated as needed. This dynamic network search has lower memory requirements compared to a search using the full static expansion of the search network. In this thesis, we investigate search methods for speech recognition using weighted finitestate transducers. The focus of this work is on dynamic search networks using on-the-fly transducer composition. We study the construction of the transducers involved and analyze different modeling approaches. Amongst other topics, we describe a novel construction of compact phone context-dependency transducers based on a joint optimization of model complexity and transducer size. We describe an efficient search algorithm and its implementation in detail and provide an experimental evaluation. The dynamic transducer-based search is compared in-depth to another state-of-the-art search strategy using dynamic network expansion, namely history conditioned lexical tree search. Experimental results are obtained using several high-performance large vocabulary continuous speech recognition systems, including systems for broadcast news and spontaneous speech in English and Arabic. This thesis includes also considerations on practical aspects of a speech recognition system. In particular, we describe a novel framework for audio segmentation and we give a detailed overview of RASR, the publicly available RWTH Aachen University speech recognition software package, which has been extended within the scope of this work.
[Impact of alcohol dependence on the course and psychopathology of schizophrenia].

AIM The study was undertaken to investigate possible influence of alcoholism on the course and psychopathology of schizophrenia. METHOD A representative sample of 61 subjects was selected from schizophrenic patients with a history of alcohol dependence (dual diagnosis) registered in the period of 1997-2000. They were compared with 60 control patients with a single diagnosis of schizophrenia. In two groups, with the interview and clinical scales, the onset, course and psychopathology of schizophrenia were assessed. RESULTS Male patients with schizophrenia and alcohol dependence had a later mean age at onset of mental illness, women--a higher rate of alcohol abuse in the family compared to the control groups. In men with dual diagnosis, the negative symptoms were less prominent. Women with schizophrenia and alcohol dependence reported more depressive symptomatology.
An optimization algorithm for the coordinated hybrid agent framework

The coordinated hybrid agent (CHA) framework for the control of multi-agent systems (MASs) has been used to model both the homogeneous and the heterogeneous multi-agent systems. In this framework, the control of the MASs is regarded as a decentralized control and coordination of agents. The CHA framework is able to implement coordination tasks for multi-agent systems. In this study, the optimization of MASs modelled by the CHA framework is studied. The time-driven dynamics and the event-driven dynamics for the optimization of a CHA system are given. The optimization problem of the MASs is analyzed. An example is also given to illustrate how to define the optimization problem for a CHA. The forward algorithm is also introduced for solving the optimization problem for a CHA system.
Dualing GANs

Generative adversarial nets (GANs) are a promising technique for modeling a distribution from samples. It is however well known that GAN training suffers from instability due to the nature of its saddle point formulation. In this paper, we explore ways to tackle the instability problem by dualizing the discriminator. We start from linear discriminators in which case conjugate duality provides a mechanism to reformulate the saddle point objective into a maximization problem, such that both the generator and the discriminator of this ‘dualing GAN’ act in concert. We then demonstrate how to extend this intuition to non-linear formulations. For GANs with linear discriminators our approach is able to remove the instability in training, while for GANs with nonlinear discriminators our approach provides an alternative to the commonly used GAN training algorithm.
Wellness assessment through environmental sensors and smartphones

Wellness is an affective state that plays a significant role in our everyday lives, influencing our behaviour, social communication and performance, and even more. Although technological advancements are used to help our society to become more health conscious, wellness and mental health is still lacking in adequate resources, particularly among the student population. In this study, we collected data from 21 participants using mobile sensors and phones. The mobile sensors collected data regarding the temperature, humidity and luminosity of the environment, while the phone provide location information and data processing. The experimental data were analyzed through Perceived Stress Scale (PSS), Pittsburgh Sleep Quality Index (PSQI) and General Well-Being Scale (GWBS). We assess the impact of the location on PSS and PSQI, and the impact of environmental conditions on GWBS. According to experimental results and correlation analysis among the data, luminosity has stronger impact on the wellness than the other two environmental parameters.
Action-Affect-Gender Classification Using Multi-task Representation Learning

Recent work in affective computing focused on affect from facial expressions, and not as much on body. This work focuses on body affect. Affect does not occur in isolation. Humans usually couple affect with an action; for example, a person could be running and happy. Recognizing body affect in sequences requires efficient algorithms to capture both the micro movements that differentiate between happy and sad and the macro variations between different actions. We depart from traditional approaches for time-series data analytics by proposing a multi-task learning model that learns a shared representation that is well-suited for action-affect-gender classification. For this paper we choose a probabilistic model, specifically Conditional Restricted Boltzmann Machines, to be our building block. We propose a new model that enhances the CRBM model with a factored multi-task component that enables scaling over larger number of classes without increasing the number of parameters. We evaluate our approach on two publicly available datasets, the Body Affect dataset and the Tower Game dataset, and show superior classification performance improvement over the state-of-the-art.