Miracle-dz/UniFAR-FTUs huggingface dataset:
Post-translational Serine/Threonine Phosphorylation and Lysine Acetylation: A Novel Regulatory Aspect of the Global Nitrogen Response Regulator GlnR in S. coelicolor M145

Soil-dwelling Streptomyces bacteria such as S.coelicolor have to constantly adapt to the nitrogen (N) availability in their habitat. Thus, strict transcriptional and post-translational control of the N-assimilation is fundamental for survival of this species. GlnR is a global response regulator that controls transcription of the genes related to the N-assimilation in S. coelicolor and other members of the Actinomycetales. GlnR represents an atypical orphan response regulator that is not activated by the phosphorylation of the conserved aspartate residue (Asp 50). We have applied transcriptional analysis, LC-MS/MS analysis and electrophoretic mobility shift assays (EMSAs) to understand the regulation of GlnR in S. coelicolor M145. The expression of glnR and GlnR-target genes was revisited under four different N-defined conditions and a complex N-rich condition. Although, the expression of selected GlnR-target genes was strongly responsive to changing N-concentrations, the glnR expression itself was independent of the N-availability. Using LC-MS/MSanalysis we demonstrated that GlnR was post-translationally modified. The post-translational modifications of GlnR comprise phosphorylation of the serine/threonine residues and acetylation of lysine residues. In the complex N-rich medium GlnR was phosphorylated on six serine/threonine residues and acetylated on one lysine residue. Under defined N-excess conditions only two phosphorylated residues were detected whereas under defined N-limiting conditions no phosphorylation was observed. GlnR phosphorylation is thus clearly correlated with N-rich conditions. Furthermore, GlnR was acetylated on four lysine residues independently of the N-concentration in the defined media and on only one lysine residue in the complex N-rich medium. Using EMSAs we demonstrated that phosphorylation inhibited the binding of GlnR to its targets genes, whereas acetylation had little influence on the formation of GlnR-DNA complex. This study clearly demonstrated that GlnR DNA-binding affinity is modulated by post-translational modifications in response to changing N-conditions in order to elicit a proper transcriptional response to the latter.
Derivatives of Spectral Functions

A spectral function of a Hermitian matrix X is a function which depends only on the eigenvalues of X, λ1X ≥ λ2X ≥. ≥ λnX, and hence may be written fλ1X, λ2X,. , λnX for some symmetric function f. Such functions appear in a wide variety of matrix optimization problems. We give a simple proof that this spectral function is differentiable at X if and only if the function f is differentiable at the vector λX, and we give a concise formula for the derivative. We then apply this formula to deduce an analogous expression for the Clarke generalized gradient of the spectral function. A similar result holds for real symmetric matrices.
TP53 Mutations in Nonsmall Cell Lung Cancer

The tumor suppressor gene TP53 is frequently mutated in human cancers. Abnormality of the TP53 gene is one of the most significant events in lung cancers and plays an important role in the tumorigenesis of lung epithelial cells. Human lung cancers are classified into two major types, small cell lung cancer (SCLC) and nonsmall cell lung cancer (NSCLC). The latter accounts for approximately 80% of all primary lung cancers, and the incidence of NSCLC is increasing yearly. Most clinical studies suggest that NSCLC with TP53 alterations carries a worse prognosis and may be relatively more resistant to chemotherapy and radiation. A deep understanding of the role of TP53 in lung carcinogenesis may lead to a more reasonably targeted clinical approach, which should be exploited to enhance the survival rates of patients with lung cancer. This paper will focus on the role of TP53 in the molecular pathogenesis, epidemiology, and therapeutic strategies of TP53 mutation in NSCLC.
Semantic Intertwine: The anathema of Mathematics

The recent scientific observation that human information processing involves four independent data types, has pinpointed a source of fallacious arguments within many domains of human thought. Our species-unique ability to assign observable characteristics to purely conceptual entities has created beautiful poetry and literature. However, this ability to generate ‘Semantic Intertwine’ has also created our most incomprehensible paradoxes and conundrums. Semantic Intertwine can be created between, or within, Semantic Categories; and in either case it then lies at the heart of fallacious, yet often very persuasive, reasoning. This paper describes how to detect mathematically-related Semantic Intertwine in erroneous arguments involving: operands (VIII), mathematical induction (VIIA), orthogonal axiom sets (VIIB), continuous functions (VIIA), exclusive disjunction (VIIA), propositional calculus (VI) and the hitherto thorny problems arising from ambiguous intra-category use of ‘infinity’ (VIIB).
Priming Adipose-Derived Mesenchymal Stem Cells with Hyaluronan Alters Growth Kinetics and Increases Attachment to Articular Cartilage

Background. Biological therapeutics such as adipose-derived mesenchymal stem cell (MSC) therapy are gaining acceptance for knee-osteoarthritis (OA) treatment. Reports of OA-patients show reductions in cartilage defects and regeneration of hyaline-like-cartilage with MSC-therapy. Suspending MSCs in hyaluronan commonly occurs in animals and humans, usually without supporting data. Objective. To elucidate the effects of different concentrations of hyaluronan on MSC growth kinetics. Methods. Using a range of hyaluronan concentrations, we measured MSC adherence and proliferation on culture plastic surfaces and a novel cartilage-adhesion assay. We employed time-course and dispersion imaging to assess MSC binding to cartilage. Cytokine profiling was also conducted on the MSC-secretome. Results. Hyaluronan had dose-dependent effects on growth kinetics of MSCs at concentrations of entanglement point (1 mg/mL). At higher concentrations, viscosity effects outweighed benefits of additional hyaluronan. The cartilage-adhesion assay highlighted for the first time that hyaluronan-primed MSCs increased cell attachment to cartilage whilst the presence of hyaluronan did not. Our time-course suggested patients undergoing MSC-therapy for OA could benefit from joint-immobilisation for up to 8 hours. Hyaluronan also greatly affected dispersion of MSCs on cartilage. Conclusion. Our results should be considered in future trials with MSC-therapy using hyaluronan as a vehicle, for the treatment of OA.
Aristotle's semantic theory and some implications for research

The study of meaning is a perennial pursuit in philosophy and linguistics. For example, in the early twentieth century logical positivists were preoccupied with problems of meaning, especially in science. And in descriptive linguistics, morphemes, the minimal meaningful linguistic units, are the object of morphological analysis. This topic, in one form or another, is also currently of interest to researchers and theorists in communication, psychology, and social psychology (Aitchinson, 1994; Bowers, Elliott, & Desmond, 1977; Bradac, 2001; Brown, 1958; Osgood, May, & Miron, 1975; Rosch, 1975). Since Aristotle studied everything, it is not particularly surprising that he had fully formed ideas about the relationship between words and referents, traditionally labeled “semantics. ” In the last fifty years or so, the study of pragmatics has arisen to complement semantic study; this is the investigation of how utterances and their meanings acquire force, why particular utterances count as particular speech acts. On a rainy day, “It’s a wonderful day for a picnic” may well be perceived as an instance of irony (Colston, 1997, 2000). As far as I can tell, Aristotle’s pragmatic ideas, such as they are, are largely treated in his Rhetoric (Aristotle, trans. 1932), which among the many Aristotelian texts cited by Modrak in Aristotle’s Theory of Language and Meaning is absent, perhaps surprisingly. However, Modrak might suggest that Aristotle’s ideas about semantics per se are chiefly presented in other works. I will return to the Rhetoric below. In this review, I will initially overview the contents of Modrak’s book to give a specific sense of the topics she covers and the arguments she makes. THE REVIEW OF COMMUNICATION 3.1 (January 2003): 41–52  2003 National Communication Association
Heart failure in rats causes changes in skeletal muscle morphology and gene expression that are not explained by reduced activity.

In patients with congestive heart failure, skeletal muscle is characterized by a smaller proportion of slow-twitch oxidative fibers and reduced oxidative enzyme activity. However, whether these changes result from disuse or occur as a direct consequence of heart failure is unresolved. To address this issue, 18 rats with heart failure 8 weeks after left coronary artery ligation and 13 sham-operated control rats underwent quantification of locomotor activity by a photocell activation technique, measurements of hemodynamics and infarct size, histochemical and morphological analyses of the soleus and plantaris muscles, and Northern analyses of muscle contractile protein and oxidative enzyme mRNA expression. Although the rats with heart failure had elevated left ventricular end-diastolic pressures (24.1 +/- 2.6 mm Hg) and a mean infarct size of 35.1 +/- 4.1%, activity levels were similar to those found in the sham-operated rats (3849 +/- 304 versus 3526 +/- 130 counts per hour). With heart failure, there was a significant reduction of type I fibers in the soleus muscle and type IIa fibers in the plantaris muscle, with corresponding increases in intermediate staining of type IIab fibers in both muscles. This was associated with a 17% decrease in citrate synthase activity in both the soleus and plantaris muscles (26.2 +/- 1.6 versus 30.7 +/- 3.4 and 29.1 +/- 2.4 versus 35.7 +/- 3.4 mumol/L per minute per gram, respectively [P < .05]). In the soleus muscle, mRNA for both beta-myosin heavy chains and cytochrome C oxidase III (normalized to 18S RNA) was reduced (0.27 +/- 0.02 versus 0.65 +/- 0.02 and 0.23 +/- 0.04 versus 0.64 +/- 0.02 U), whereas the messages for IIx and IIb myosin heavy chains were increased. A similar decrease in messages for cytochrome oxidase and the primary myosin isoform was observed in the plantaris muscle. Both soleus beta-myosin heavy chain and cytochrome C oxidase expression show significant inverse relationships to left ventricular end-diastolic pressure and infarct size. In contrast, there was no relationship between either beta-myosin heavy chain or cytochrome C oxidase expression and locomotor activity. These results indicate that in rats heart failure produces changes in skeletal muscle gene expression at the pretranslational level that cannot be explained by inactivity.
Different Specialties, Different Gaze Strategies: Eye Tracking Opportunities in Seismic Interpretation Context

Identifying how geoscientists interact with seismic images allows a deeper understanding of their rationale and the seismic interpretation process itself. Moreover, identifying nuances involving seismic interpreters performing slightly different roles opens new possibilities relative to how decision support systems could become part of the seismic interpretation. In this work, we detail an eye tracking study involving 11 seismic interpreters interacting with two seismic images. The results show that seismic interpreters, with different specialties, interact with seismic images differently. From the results, it is possible to better characterize gaze strategies from different seismic interpreters, which could also be used as input information for decision support systems.
Disconnect: A Proposal for Reclaiming Control in HCI

As the lines between the digital and analog worlds become increasingly blurred, it is nearly impossible to traverse modern life without creating a digital footprint. This integration is so deep-rooted into the fabric of society, that if one attempted to choose to disconnect from today's hyperconnected world, one would have to move away from civilization. Weiser's vision of the omni-present, ubiquitous computer of the 21st century [21] has been realized, but at a cost. With invisible interfaces we forego the ability to recognize when we are being watched, heard or influenced by external actors. This paper takes a bottom-up approach of using design fiction narratives to explore how to design mechanisms of control (MoC) that may help reinstate human control and agency over our data. Preliminary results show emergent themes pertaining to data access, governance and sharing; the forms of MoC; as well as methodological lessons.
Landmark-Based Registration Using a Local Radial Basis Function Transformation 1

In this paper we propose the use of a local image transformation involving radial basis functions for landmark-based registration of medical images. More precisely, we consider radial basis functions as nodal functions in the modified Shepard method. In this way we obtain an image transformation more accurate and stable than the one given by the global radial basis functions, as shown by numerical results. c ⃝ 2011 European Society of Computational Methods in Sciences and Engineering
Efficacy and safety of duloxetine in Chinese breast cancer patients with paclitaxel-induced peripheral neuropathy.

Objective Chemotherapy with paclitaxel is associated with significant neurotoxicity that may offset patients' quality of life and therapeutic benefits. This prospective, non-randomized control study evaluated the efficacy and safety of an antidepressant drug, duloxetine, at 30 or 60 mg/d, in the treatment of paclitaxel-induced peripheral neuropathy (PIPN) in Chinese breast cancer patients. Methods A total of 102 patients with a median age of 50 (range, 25-60) years, treated in the Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, between November 2014 and January 2017 were finally enrolled. Stratified by baseline characteristics, the patients were classified into two groups, receiving either duloxetine or alternative anti-neurotoxicity drugs. During the course of the paclitaxel regimen, the eligibility criteria included sensory neuropathy, as evaluated by the National Cancer Institute-Common Toxicity Criteria for Adverse Events. The treatment consisted of receiving 30 mg duloxetine (for the first 4 weeks) and 60 mg duloxetine for an additional 8 weeks, or any other anti-neurotoxicity drug daily during the same crossover period. The improvement associated with PIPN from the patient's perspective were assessed by the Functional Assessment of Cancer Therapy-Taxane (FACT-Tax) Scales, which contained questions scored from 0 to 4 (0, not at all; 4, very much; total score range, 0-44). Results Duloxetine was more effective in decreasing PIPN (odds ratio=5.426; 95% confidence interval, 1.898-15.514; P=0.002). Between duloxetine group and control group, the median (25th-75th percentiles) decreasing difference in the FACT-Tax pain score was 4 (2-6) vs. 1 (0-4) (P=0.005). Conclusions Duloxetine is a promising and safe option with tolerable toxicity at a dose of 60 mg/d for Chinese breast cancer patients with PIPN. Non-neuropathy adverse events were mild and similar in both groups. The major toxicities of duloxetine included nausea, constipation, somnolence, dizziness and distention of the eyes. Further examination of the benefits of duloxetine in the prevention of PIPN is required.
Let's Chat in Alipay: Understanding Social Function Usage in Task-oriented Apps

Recently, many mobile apps start to incorporate social functions into their design, even for the task-oriented ones, i.e., those designed mainly to help users complete certain tasks. For instance, Taobao, a shopping app, includes online-sharing and instant-messaging functions. However, there is still lack of research on how the users accept and use these social functions. This paper aims to unveil the user requirements on the social functions in task-oriented apps, and accordingly provide design suggestions for app developers. To this end, we conduct semi-structured interviews with 16 participants on how they use instant-messaging functions in three widely-used task-oriented apps, the shopping app Taobao, an online payment app Alipay, and an entertainment app NetEase Cloud Music. Our findings demonstrate that the instant-messaging functions in these apps are not widely accepted, although they benefit user experience and facilitate users' online social activities. We show that both the design and the users' stereotype towards the apps are important reasons. Finally, we suggest several design guidelines.
Call Me by My Name: Exploring Roles of Sci-fi Voice Agents

Voice Conversational Agents (VCAs) are increasingly becoming part of our daily life. Calling them by their names can solve more than just a problem of efficiency in interaction between users and VCAs, but also can cast them as actors capable of playing a role in a relationship. However, due to the immature state of the technology and its related services, such relationships between users and VCAs can be limited in practice. To broaden the scope in designing different relationships, this study explores VCAs depicted in sci-fi movies. Sci-fi is not purely based on fantasy, but also is a social reflection on technology, which in turn can inspire design researchers to understand and speculate the complexity of VCAs. Through community sourcing with sci-fi enthusiasts, 43 Sci-fi VCAs were deduced. A movie event was also organized to discuss the role of VCAs. Finally, this paper presents several possible design insights for designing the role of VCAs.
Assessment of Physical Water Scarcity in Africa Using GRACE and TRMM Satellite Data

The critical role of water in enabling or constraining human well-being and socioeconomic activities has led to an interest in quantitatively establishing the status of water (in)sufficiency over space and time. Falkenmark introduced the first widely accepted measure of water status, the Water Scarcity Index (WSI), which expressed the status of the availability of water resources in terms of vulnerability, stress, and scarcity. Since then, numerous indicators have been introduced, but nearly all adopt the same basic formulation; water status is a function of “available water” resource—by the demand or use. However, the accurate assessment of “available water” is difficult, especially in data-scarce regions, such as Africa. In this paper, therefore, we introduce a satellite-based Potential Available Water Storage indicator, PAWS. The method integrates GRACE (Gravity Recovery and Climate Experiment) satellite Total Water Storage (TWS) measurements with the Tropical Rainfall Measuring Mission (TRMM) precipitation estimates between 2002 and 2016. First, we derived the countries’ Internal Water Storage (IWS) using GRACE and TRMM precipitation data. Then, the IWS was divided by the population density to derive the PAWS per capita. Following the Falkenmark thresholds, 54% of countries are classified in the same water vulnerability status as the AQUASTAT Internal Renewable Water Resources (IRWR) method. Of the remaining countries, PAWS index leads to one or two categories shift (left or right) of water status. The PAWS index shows that 14% (~160 million people) of Africa’s population currently live under water scarcity status. With respect to future projections, PAWS index suggests that a 10% decrease in future water resources would affect ~37% of Africa’s 2025 population (~600 million people), and 57% for 2050 projections (~1.4-billion people). The proposed approach largely overcomes the constraints related to the data needed to rapidly and robustly estimate available water resources by incorporating all stocks of water within the country, as well as underscores the recent water storage dynamics. However, the estimates obtained concern potential available water resources, which may not be utilizable for practical, economic, and technological issues.
Dual-Tree Complex Wavelet Transform in the Frequency Domain and an Application to Signal Classification

We examine Kingsbury's dual-tree complex wavelet transform in the frequency domain, where it can be formulated for standard wavelet filters without special filter design and apply the method to the classification of signals. The obtained transforms achieve low shift sensitivity and better directionality compared to the real discrete wavelet transform while retaining the perfect reconstruction property.
iScream!: Towards the Design of Playful Gustosonic Experiences with Ice Cream

In this demonstration, we present iScream! , a novel gustosonic experience that generates unique digital sounds as a result of eating ice cream. The system uses capacitive sensing to detect eating actions and based on these actions, it plays out six different playful sounds to facilitate a playful eating experience. Our aim is to support a playful way of eating because we believe that interactive technology offers unique opportunities to facilitate novel engaging eating experiences. Ultimately, with this work, we aim to inspire and guide designers working with interactive playful gustosonic experiences, which open up new interaction possibilities to experience eating as play.
Relative influences: patterns of HPA axis concordance during triadic family interaction.

OBJECTIVE Within-family concordance in physiology may have implications for family system functioning and for individual health outcomes. Here, we examine patterns of association in cortisol within family triads. METHODS A total of 103 adolescents and their parents sampled saliva at multiple timepoints before and after a conflict discussion task. We explored whether within-family associations existed and were moderated by stepparent presence and youth gender, and whether within-family patterns of influence correlated with individuals' aggregate cortisol. RESULTS Across the laboratory visit, the cortisol levels of fathers, mothers, and youth were positively associated. In time-lagged models, mothers' cortisol predicted fathers' cortisol levels sampled at the following timepoint, whereas fathers' predicted youths' and youths' predicted mothers' cortisol. These patterns appeared stronger in families not including stepparents. Youth gender moderated some associations: in the aggregate, youth were more strongly linked with their same-gender parent. In time-lagged models, girls were more closely linked to their mothers than boys, and both parents were more linked to girls. Youth showed higher aggregate cortisol output if they were more linked with their mothers, and lower output if more linked with their fathers; parents had higher output if they were more linked with their spouses and lower output if more linked with their children. CONCLUSIONS These results suggest that family members' physiological activation may be linked during shared interaction, and that these patterns may be affected by family role and by youth gender. Our findings identify specific patterns of physiological influence within families that may inform family systems theories.