Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimation of Activity Related Energy Expenditure and Resting Metabolic Rate in Freely Moving Mice from Indirect Calorimetry Data

Physical activity (PA) is a main determinant of total energy expenditure (TEE) and has been suggested to play a key role in body weight regulation. However, thus far it has been challenging to determine what part of the expended energy is due to activity in freely moving subjects. We developed a computational method to estimate activity related energy expenditure (AEE) and resting metabolic rate (RMR) in mice from activity and indirect calorimetry data. The method is based on penalised spline regression and takes the time dependency of the RMR into account. In addition, estimates of AEE and RMR are corrected for the regression dilution bias that results from inaccurate PA measurements. We evaluated the performance of our method based on 500 simulated metabolic chamber datasets and compared it to that of conventional methods. It was found that for a sample time of 10 minutes the penalised spline model estimated the time-dependent RMR with 1.7 times higher accuracy than the Kalman filter and with 2.7 times higher accuracy than linear regression. We assessed the applicability of our method on experimental data in a case study involving high fat diet fed male and female C57Bl/6J mice. We found that TEE in male mice was higher due to a difference in RMR while AEE levels were similar in both groups, even though female mice were more active. Interestingly, the higher activity did not result in a difference in AEE because female mice had a lower caloric cost of activity, which was likely due to their lower body weight. In conclusion, TEE decomposition by means of penalised spline regression provides robust estimates of the time-dependent AEE and RMR and can be applied to data generated with generic metabolic chamber and indirect calorimetry set-ups.
Cost Saving Opportunities in NSCLC Therapy by Optimized Diagnostics

With an incidence of 68 new cases per 100,000 people per year, an estimated total number of up to 350,000 new non-small-cell lung cancer (NSCLC) cases are diagnosed each year in the European Union. Up to 10% of NSCLC patients are eligible for therapy with novel ALK (anaplastic lymphoma kinase) inhibitors, as they have been diagnosed with a mutation in the gene coding for ALK. The ALK inhibitor therapy costs add up to approx. 9000 € per patient per month, with treatment durations of up to one year. Recent studies have shown that up to 10% of ALK cases are misdiagnosed by nearly 40% of pathologic investigations. The current state-of-the-art ALK diagnostic procedure comprises a Fluorescent in situ Hybridization (FISH) assay accompanied by ALK inhibitor therapy (Crizotinib). The therapy success ranges between a full therapy failure and the complete remission of the tumor (i.e., healing), but the biomedical and systemic reasons for this range remain unknown so far. It appears that the variety of different ALK mutations and variants contributes to the discrepancy in therapy results. Although the major known fusion partner for ALK in NSCLC is the Echinoderm microtubule-associated protein-like 4 (EML4), of which a minimum of 15 variants have been described, an additional 20 further ALK fusion variants with other genes are known, of which three have already been found in NSCLC. We hypothesize that the wide variety of known (and unknown) ALK mutations is associated with a variable therapy success, thus rendering current companion diagnostic procedures (FISH) and therapy (Crizotinib) only partly applicable in ALK-related NSCLC treatment. In cell culture, differing sensitivity to Crizotinib has been shown for some fusion variants, but it is as yet unknown which of them are really biologically active in cancer patients, and how the respective variants affect the response to Crizotinib treatment. Moreover, it has been demonstrated that translocated ALK genes can also be observed in healthy tissues and are not compulsorily associated with tumors. Therefore, it is important to keep in mind that even for the known variants of ALK fusion genes, the biological function is not known for all variants, and that no information is available on the homogeneity of ALK fusion variants within a single tumor. These facts, in concert with data for ALK mutation prevalence and therapy outcomes of a German cohort of NSCLC patients, support the hypothesis that, by using novel companion diagnostic tools in combination with therapy outcome predictions, massive cost savings could be possible in European Health Care systems without a loss of patient care.
Emotional speaker verification based on i-vectors

Recently i-vectors approach in speaker verification become very successful and popular. The i-vectors principle is based on representation of each utterance by low-dimensional feature vector of fixed length. In this experiment for purposes of speaker recognition emotional speech database was applied. Using the i-vector principle two concepts of speaker model training were performed. In the process of features extraction the Mel Frequency Cepstral Coefficients (MFCC) with different number of coefficients in combination with coefficient of log energy, the first, second and third regression coefficients were used. Mahalanobis distance metric and Cosine Distance Scoring (CSS) metric were used for classification of the speaker recognition in this paper. In this work our own emotional database - SUS - of recordings in Slovak language was introduced. Utterances of male speakers of mentioned corpus were used as an input to the verification system.
In Praise of Numerical Computation

Theoretical Computer Science has developed an almost exclusively discrete/algebraic persona. We have effectively shut ourselves off from half of the world of computing: a host of problems in Computational Science & Engineering (CS&E) are defined on the continuum, and, for them, the discrete viewpoint is inadequate. The computational techniques in such problems are well-known to numerical analysis and applied mathematics, but are rarely discussed in theoretical algorithms: iteration, subdivision and approximation. By various case studies, I will indicate how our discrete/algebraic view of computing has many shortcomings in CS&E. We want embrace the continuous/analytic view, but in a new synthesis with the discrete/algebraic view. I will suggest a pathway, by way of an exact numerical model of computation, that allows us to incorporate iteration and approximation into our algorithms’ design. Some recent results give a peek into how this view of algorithmic development might look like, and its distinctive form suggests the name “numerical computational geometry” for such activities. You might object that it would be reasonable enough for me to try to expound the differential calculus, or the theory of numbers, to you, because the view that I might find something of interest to say to you about such subjects is not prima facie absurd; but that geometry is, after all, the business of geometers, and that I know, and you know, and I know that you know, that I am not one; and that it is useless for me to try to tell you what geometry is, because I simply do not know. — G.H. Hardy, in “What is Geometry? ” 1925 Presidential Address to the Mathematical Association
Parent and Friend Social Support and Adolescent Hope

The purpose of this study was to conduct two meta-analyses. The first examined social support from parents in relation to adolescent hope, and the second examined social support from friends in relation to adolescent hope. Using Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for the literature reviewed, nine published studies or doctoral dissertations completed between 1990 and 2014 met the inclusion criteria. Using meta-analytic techniques and the mean weighted r statistic, the results indicated that social support from friends had a stronger mean effect size (ES = .31) than social support from parents (ES = .21); there was a statistically significant difference between the two ESs. Two of the four moderators for the parent social support–adolescent hope relationship were statistically significant. They were quality score and health status. Implications for school nurses and nurses in all settings are addressed, and conclusions are drawn based on the findings.
System-level Optimizations for Memory Access in the Execution Migration Machine ( EM 2 )

In this paper, we describe system-level optimizations for the Execution Migration Machine (EM2), a novel shared-memory architecture to address the memory wall and scalability issues for large-scale multicores. In EM2, data is never replicated and threads always migrate to the core where data is statically stored. This enables EM2 not only to provide cache coherence without any complex protocols or expensive directories, but also to better utilize on-chip cache and thus experience much lower cache miss rate. However, it may incur significant execution migrations for shared data, which increases memory latency and network traffic, and thus, keeping migration rates low is a key under EM2. We present systematic application optimization techniques to address this problem for EM2 suitable for a compiler/OS implementation. Applying these optimizations manually to parallel benchmarks from the SPLASH-2 suite, we dramatically reduce the average migration rate for EM2 by 53%, which directly improves parallel completion time by 34% on average. This allows EM2 to perform competitively compared to a traditional cache-coherent architecture, on a conventional electrical network.
Traditional Chinese medicine baoxin decoction improves cardiac fibrosis of rats with dilated cardiomyopathy

We investigated the effect of baoxin decoction (BXD) on myocardial fibrosis and clarified the possible mechanism of action. Dilated myocardiopathy was induced by doxorubicin injected intraperitoneally for 6 weeks. Rats that demonstrated dilated myocardiopathy were randomly divided into five groups plus a control group. Three groups were treated with BXD (7.5/kg, 15 g/kg and 30 g/kg) daily for 4 weeks. One group was treated with 8.75 g/kg of captopril (positive control), and with physiologic saline (negative control). Cardiac function was evaluated using echocardiography. Hematoxylin and eosin, and Massons trichrome staining were performed, PICP and PIIINP were assessed by ELISA, the expression of galectin-3 and collagen types I and III was evaluated with reverse transcription-quantitative PCR, and interrelated proteins were detected by western blot analysis. BXD downregulated galectin-3, collagen I and III and was correlated with a high expression of fibrosis markers. It also significantly decreased myocardial collagen volume fraction (CVF), together with markedly preventing the upregulation of collagen I and III. In addition, BXD downregulated the expression of TGF-β1 and Smad3 in the myocardial fibrosis rats. Therefore, BXD treatment significantly improved cardiac function and alleviated myocardial fibrosis in a rat model of doxorubicin-induced dilated cardiomyopathy (DCM), which is the mechanism that may be associated with inhibiting the TGF-β1 signaling pathway.
Building a unified repository of interaction patterns

In recent years there have been many proposals of lists of interaction patterns applicable to the design and development of web interfaces. Many of the patterns proposed in different lists are the same, perhaps with different names and different examples. Our purpose is to join these lists in a unified repository. This requires formalizing the definition of interaction patterns to make them comparable, facilitate their classification or recommend them automatically based on a characterization of user needs, interaction context, etc. In parallel, Web applications using Semantic Web technologies are starting to proliferate. This implies in many cases a paradigm shift for user interaction that requires questioning which are the more appropriate end user tasks, starting from "traditional" Web interaction tasks but taking into account that they might change or raise new tasks. A good characterization of these tasks is then the starting point to explore what patterns can be used to implement them. To facilitate this process, we have built a unified repository of interaction patterns classified by Semantic Web end-user tasks. We have built this repository using Semantic Web technologies.
Evaluation of clinical outcomes of patients with post-stroke wrist and finger spasticity after ultrasonography-guided BTX-A injection and rehabilitation training

Objective: Using ultrasonography (US) to guide botulinum toxin type A (BTX-A) injection in patients with post-stroke wrist and finger flexor muscle spasticity and assessing clinical outcomes after the injection and rehabilitation intervention. Methods: Twenty-three patients with wrist and finger spasticity after stroke were recruited in this study from May 2012 to May 2013. Under US guidance, the proper dose (250 U) of BTX-A was injected into each spastic muscle at two injection sites. Then, conventional rehabilitation training started next day after BTX-A injection. The degree of spasticity was assessed by modified Ashworth scale (MAS) and wrist and finger motor function by active rang of movement (AROM), and Fugl-Meyer assessment (FMA) at the baseline, 1, 2, 4 and 12 weeks after BTX-A injection. Results: Significant decreases (p < 0.02) in the MAS scores of both the finger flexor muscle tone and wrist flexor muscle tone measured at 1, 2, 4, and 12 weeks after the BTX-A injection were found in comparison with the baseline scores. Compared with the baseline, the AROM values of the wrist and finger extensions and the FMA scores of the wrist and hand significantly increased (p < 0.02) at 2, 4 and 12 weeks after the BTX-A injection. Conclusions: US-guided BTX-A injection combined with rehabilitation exercise decrease spasticity of the wrist and finger flexor muscles and improve their motor function in stroke patients up to 12 weeks following BTX-A injection.
The status of the microbial census: an update

A census is typically carried out for people at a national level; however, microbial ecologists have implemented a molecular census of bacteria and archaea by sequencing their 16S rRNA genes. We assessed how well the microbial census of full-length 16S rRNA gene sequences is proceeding in the context of recent advances in high throughput sequencing technologies. Among the 1,411,234 and 53,546 full-length bacterial and archaeal sequences sequences, 94.5% and 95.1% of the bacterial and archeaeal sequences, respectively, belonged to operational taxonomic units (OTUs) that have been observed more than once. Although these metrics suggest that the census is approaching completion, 29.2% of the bacterial and 38.5% of the archaeal OTUs have been observed more than once. Thus, there is still considerable microbial diversity to be explored. Unfortunately, the rate of new full-length sequences has been declining and new sequences are primarily being deposited by a small number of studies. Furthermore, sequences from soil and aquatic environments, which are known to be rich in bacterial diversity, only represent 7.8 and 16.5% of the census while sequences associated with zoonotic environments represent 55.0% of the census. Continued use of traditional approaches and new technologies such as single cell genomics and short read assembly are likely to improve our ability to sample rare OTUs if it is possible to overcome this sampling bias. The success of ongoing efforts to use short read sequencing to characterize microbial communities requires that researchers strive to expand the depth and breadth of the microbial census. Importance The biodiversity contained within the bacterial and archaeal domains dwarfs that of the eukaryotes and the services these organisms provide to the biosphere are critical. Surprisingly, we have done a relatively poor job of keeping track of the ongoing effort to characterize the biodiversity as represented in full-length 16S rRNA genes. By understanding how this census is proceeding, it is possible to suggest the best allocation of resources for advancing the census. We found that the ongoing effort has done an excellent job of sampling the most abundant organisms, but struggles to sample the more rare organisms. Through the use of new sequencing technologies we should be able to obtain full-length sequences from these rare organisms. Furthermore, we suggest that by allocating more resources to sampling environments known to have the greatest biodiversity we will be able to make significant advances in our characterization of microbial diversity.
AugIR: the conceptual design and evaluation of an augmented interaction room

It is often difficult for stakeholders with heterogeneous backgrounds to maintain a common understanding of the most important risk and value drivers of a complex software project. Therefore, I propose the concept of a so-called Augmented Interaction Room, i.e. a persistent physical team room whose walls are outfitted with large interactive displays. It provides a dedicated project space for supporting collaborative system design and the communication among members of a software development project. In this paper, I describe the specific challenges regarding visualization and navigation on these large displays and present my approach on how to support stakeholders by automatically identifying inconsistencies, contradictions and potential project risks.
Assessing Others' Risk‐Taking Behavior from Their Affective States: Experimental Evidence Using a Stag Hunt Game

Researchers are increasingly exploring the role of emotions in interactive decision‐making. Recent theories have focused on the interpersonal effects of emotions—the influence of the decisionmaker’s expressed emotions on observers’ decisions and judgments. In this paper, we examine whether people assess others’ risk preferences on the basis of their emotional states, whether this affects their own behavior, and how this assessment matches others’ actual behavior. To test these ideas, we used an experimental Stag Hunt game (n = 98), and included non‐trivial financial consequences. Participants were told (truthfully) that their counterparts’ previous task had left them happy, fearful, or emotionally neutral. People who were told their counterparts were fearful reported that they expected less risky decisions from these counterparts than people told their counterparts were neutral or happy. As a result, given that the Stag Hunt is a coordination game, these participants were themselves less risky. Interestingly, these participants’ expectations were not accurate; thus, coordination failed, and payoffs were low. This raises the possibility of a “curse of knowledge” whereby one player’s erroneous beliefs about the effects of the counterpart’s emotional state leads the first player to make poor action choices.
Single-spot two-dimensional displacement measurement based on self-mixing interferometry

The simultaneous and independent measurements of in-plane and out-of-plane displacements are significant issues to be solved in research. Here a novel system to realize single-spot two-dimensional (2D) displacement measurement of a noncooperative target is reported. The performance of the system is tested in the displacement measurement of an aluminum target with a rough surface. 2D random movement and 2D movement with different parameters of Lissajous figures are measured by the system. The ranges of the 2D displacement measurement reach 500 μm and the accuracies reach the submicron scale. The resolutions of the two dimensions are all better than 5 nm. The measurement system is based on laser heterodyne self-mixing interferometry with frequency multiplexing, which has advantages such as noncontact, nondestruction, nanometer-scale resolution and high sensitivity. The method is promising to be applied in 2D deformation tests of materials, 2D rotor vibration measurement, 2D positioning of particles, thermal expansion coefficient measurement, and other applications.
Delineating cooperative responses of processive motors in living cells

Significance Although many vesicles and organelles are known to be transported by groups of interacting cytoskeletal motors, the precise impact of collective motor behaviors on intracellular transport and trafficking processes remains controversial. By engineering COS-7 cells to provide genetic control over the density of motors on, and the sizes of vesicles (peroxisomes), we performed systematic comparisons of the collective behaviors of kinesin and myosinVa motors. The responses of cargo velocities, run lengths, and position fluctuations to these parameters suggest that myosinVa motors can cooperate more productively than kinesins when transporting cargos as a team. This behavior is derived from the mechanochemical properties of these motors and suggests that the collective functions of motors like myosinV can be regulated more sensitively than those of kinesin. Characterizing the collective functions of cytoskeletal motors is critical to understanding mechanisms that regulate the internal organization of eukaryotic cells as well as the roles various transport defects play in human diseases. Though in vitro assays using synthetic motor complexes have generated important insights, dissecting collective motor functions within living cells still remains challenging. Here, we show that the protein heterodimerization switches FKBP-rapalog-FRB can be harnessed in engineered COS-7 cells to compare the collective responses of kinesin-1 and myosinVa motors to changes in motor number and cargo size. The dependence of cargo velocities, travel distances, and position noise on these parameters suggests that multiple myosinVa motors can cooperate more productively than collections of kinesins in COS-7 cells. In contrast to observations with kinesin-1 motors, the velocities and run lengths of peroxisomes driven by multiple myosinVa motors are found to increase with increasing motor density, but are relatively insensitive to the higher loads associated with transporting large peroxisomes in the viscoelastic environment of the COS-7 cell cytoplasm. Moreover, these distinctions appear to be derived from the different sensitivities of kinesin-1 and myosinVa velocities and detachment rates to forces at the single-motor level. The collective behaviors of certain processive motors, like myosinVa, may therefore be more readily tunable and have more substantial roles in intracellular transport regulatory mechanisms compared with those of other cytoskeletal motors.
Optimal light harvesting in 2D semiconductor heterostructures

Optoelectronics with two dimensional (2D) heterostructures combining transition metal dichalcogenides (TMDCs) and other semiconductors in hybrid stacks is potentially promising because of the possibility of fabricating devices with high efficiency and new properties. Ultrafast charge transfer across the interface and long lifetime of carriers makes the vertical geometry attractive with respect to traditional bulk heterostructures. In such ultrathin structures, the multiple boundaries and the thickness of each material play a key role in the interaction of light with the device and can strongly influence the device performance. In this article we study light harvesting in 2D InSe/MoS2 semiconductor heterostructures by measuring Raman enhancement or attenuation as a function of layer thicknesses. Measurements are precisely reproduced by the calculation of the light emission, and the field distribution inside the heterostructure. Optimizing layer thickness and material interfaces has a significant effect on the light distribution in such 2D heterostructures with layer thickness in the region of a few tens of nanometers, providing a means to enhance the performance of emerging 2D semiconductor-heterostructure optoelectronics.