Miracle-dz/UniFAR-FTUs huggingface dataset:
Trailing the Path to Preventive Oncology

Cancer is one of the communicable diseases killing the mankind and is likely to be a global pandemic by year 2050. Fifty percent of cancers are preventable because of the causal association with modifiable risk factors. Preventive oncology is any measure that is taken to prevent development or progression of malignant process. Around one third of cancer deaths are due to the 5 leading behavioral and dietary risks: high body mass index, low fruit and vegetable intake, lack of physical activity, tobacco use, alcohol use. History of the science dates back to as early as 1912 when tobacco was coined as a culprit for lung tumors. Preventive oncology is very important not only because of its health impact but also for huge impact on economy. The total economic impact of premature death and disability from cancer was $ 895bilion in 2008 which is 1.5% of world’s Gross Domestic Product (GDP). More than 30% of cancer deaths could be prevented by modifying or avoiding key risk factors like tobacco use, obesity, unhealthy diet with low fruit and vegetable intake, lack of physical activity, alcohol use, sexually transmitted HPV-infection, infection by HBV, ionizing and non-ionizing radiation, urban air and water pollution, adulteration of food with harmful chemicals and indoor smoke from household use of solid fuels. Non modifiable risk factors like Genetic and hereditary risk factors play a role in 10% of cancers where mutations in susceptible genes are found as a part of hereditary cancer syndromes. There are various risk groups identified and risk models are available to target the population for the effective preventive measures in the community. Curtailing tobacco use, dietary and life style modification and avoiding chemical carcinogens as an occupational hazard are important aspects. Certain viruses are known to be carcinogenic. Prevention of transmission and vaccination for the same is important step forward towards prevention of diseases like hepatitis B/C and HCC, HPV and cervical and anal cancer. Screening for early detection of cancer is an important strategy for breast, cervical, lung, colorectal, prostate and skin cancers. There are chemo-preventive agents for risk reduction for certain risk groups like tamoxifen, raloxifen, aspirin, finasteride and vitamin D. Surgical risk reduction is recommended for certain genetic syndromes. Preventive oncology is the future of oncology as we come to know more and more about the etiological aspects, understand molecular epidemiology and molecular basis of the dreadful disease. This is the only way out to tackle the cancer which is slowly and silently becoming a pandemic.
Drosophila mef2 expression during mesoderm development is controlled by a complex array of cis-acting regulatory modules.

The function of the Drosophila mef2 gene, a member of the MADS box supergene family of transcription factors, is critical for terminal differentiation of the three major muscle cell types, namely somatic, visceral, and cardiac. During embryogenesis, mef2 undergoes multiple phases of expression, which are characterized by initial broad mesodermal expression, followed by restricted expression in the dorsal mesoderm, specific expression in muscle progenitors, and sustained expression in the differentiated musculatures. In this study, evidence is presented that temporally and spatially specific mef2 expression is controlled by a complex array of cis-acting regulatory modules that are responsive to different genetic signals. Functional testing of approximately 12 kb of 5' flanking region of the mef2 gene showed that the initial widespread mesodermal expression is achieved through a 280-bp twist-dependent enhancer. The subsequent dorsal mesoderm-restricted mef2 expression is mediated through a 460-bp dpp-responsive regulatory module, which involves the function of the Smad4 homolog Medea and contains several binding sites for Medea and Mad. The analysis also showed that regulated mef2 expression in the caudal and trunk visceral mesoderm, which give rise to longitudinal and circular gut musculatures, respectively, is under the control of distinct enhancer elements. In addition, mef2 expression in the cardioblasts of the heart is dependent upon at least two distinct enhancers, which are active at different periods during embryogenesis. Moreover, multiple regulatory elements are differentially activated for specific expression in presumptive muscle founders, prefusion myoblasts, and differentiated muscle fibers. Taken together, the presented data suggest that specific expression of the mef2 gene in myogenic lineages in the Drosophila embryo is the result of multiple genetic inputs that act in an additive manner upon distinct enhancers in the 5' flanking region.
Interaction between Saikosaponin D, Paeoniflorin, and Human Serum Albumin

Saikosaponin D (SSD) and paeoniflorin (PF) are the major active constituents of Bupleuri Radix and Paeonia lactiflora Pall, respectively, and have been widely used in China to treat liver and other diseases for many centuries. We explored the binding of SSD/PF to human serum albumin (HSA) by using fluorospectrophotometry, circular dichroism (CD) and molecular docking. Both SSD and PF produced a conformational change in HSA. Fluorescence quenching was accompanied by a blue shift in the fluorescence spectra. Co-binding of PF and SSD also induced quenching and a conformational change in HSA. The Stern-Volmer equation showed that quenching was dominated by static quenching. The binding constant for ternary interaction was below that for binary interaction. Site-competitive experiments demonstrated that SSD/PF bound to site I (subdomain IIA) and site II (subdomain IIIA) in HSA. Analysis of thermodynamic parameters indicated that hydrogen bonding and van der Waals forces were mostly responsible for the binary association. Also, there was energy transfer upon binary interaction. Molecular docking supported the experimental findings in conformation, binding sites and binding forces.
Immunogenic cell death biomarkers HMGB1, RAGE, and DNAse indicate response to radioembolization therapy and prognosis in colorectal cancer patients

Radioembolization therapy (RE) is an efficient locoregional treatment for liver metastases from colorectal cancer. Serum biomarkers involved in immunogenic cell death are potentially valuable for early predicting therapy response and estimating prognosis. In a prospective observation study, blood samples were taken from 49 consecutive colorectal cancer patients with extensive hepatic metastases before, 24 and 48 hr after RE. Serum levels of high mobility group box 1 (HMGB1), receptor of glycation end products (RAGE) and activity of desoxyribonuclease were compared with response to therapy regularly determined radiologically 3 months after therapy and with overall survival. Serum levels of HMGB1 were increased already 24 hr after RE, while RAGE levels were decreased and DNAse remained unchanged. In radiological staging, 35 patients demonstrated disease progression while 14 patients had stable disease or remission. Serum HMGB1 levels 24 hr after RE were significantly higher in progressive than in nonprogressive patients while for RAGE and DNAse no difference was observed between the response groups. Concerning overall survival, high pretherapeutic (0 hr) and 24 hr levels of HMGB1 were associated with poor outcome. Multivariate analysis including HMGB1, tumor, liver and inflammation markers revealed HMGB1 and CRP as independent prognostic parameters. HMGB1 is a valuable serum biomarker for early estimation of therapy response and prognosis in colorectal cancer patients with liver metastases undergoing RE therapy.
Transition from the Z2 spin liquid to antiferromagnetic order: spectrum on the torus

We describe the finite-size spectrum in the vicinity of the quantum critical point between a Z2 spin liquid and a coplanar antiferromagnet on the torus. We obtain the universal evolution of all low-lying states in an antiferromagnet with global SU(2) spin rotation symmetry, as it moves from the 4-fold topological degeneracy in a gapped Z2 spin liquid to the Anderson “tower-of-states” in the ordere da ntiferromagnet. Due to the existence of nontrivial order on either side of thi st ransition, this critical point cannot be described in a conventional Landau-Ginzburg-Wilson framework. Instead it is described by a theory involving fractionalized degrees of freedom known as the O(4) ∗ model, whose spectrum is altered in a significant way by its proximity to a topologically ordered phase. We compute the spectrum by relating it to the spectrum of the O(4) Wilson-Fisher fixed point on the torus, modified with a selection rule on the states, and with nontrivial boundary conditions corresponding to topological sectors in the spin liquid. The spectrum of the critical O(2N )m odel is calculated directly atN = ∞ ,w hich then allows ar econstruction of the full spectrum of the O(2N) ∗ model at leading order in 1/N . T his spectrum is au nique characteristic of the vicinity of a fractionalizedquantum critical point, as well as a universal signature of the existence of proximate Z2 topological and antiferromagnetically-ordered phases, and can be compared with numerical computations on quantum antiferromagnets on two dimensional lattices.
Cognitive Distortions and Adolescent Affective Disorder

Despite a proliferation of recent research examining childhood and adolescent depression, the area still lags behind the adult depression field, particularly in the investigation of cognitive correlates of affective psychopathology. To advance cognitive research with youth, the Children's Negative Cognitive Error Questionnaire (CNCEQ) was developed to provide a measure of cognitive distortions or errors in children and adolescents. Yet, few studies have employed the CNCEQ and no evidence exists supporting the validity of its four component cognitive error scales. The purpose of the present study was to examine the construct validity of the CNCEQ and its constituent scales through the use of factor analysis and criterion-group comparisons. Groups of adolescent psychiatric inpatients, diagnosed as affective or disruptive disordered, completed the CNCEQ following admission. Results failed to support the implicit four-factor structure of the CNCEQ, instead suggesting the appropriateness of a single-factor solution labeled "negative thinking. " Despite no diagnostic group differences on the CNCEQ total or other scale scores, affective disordered patients evinced more cognitive errors on the Overgeneralizing scale. Findings suggest that the CNCEQ in its current stage of development holds promise, yet requires refinement to produce a valid measure of cognitive functioning in youth.
The projections of cells in different layers of the cat's visual cortex

The projection of cells in different layers of several cortical visual areas in the cat were studied using the method of retrograde transport of horseradish peroxidase. Injections of the enzyme were made through a recording micropipette, making it possible to localize the injection site by physiological criteria. We found that layer VI cells projected to the lateral geniculate nucleus, while a distinct population of cells in layer V projected to the superior colliculus. Cells in layers II and III were the major sources of ipsilateral cortico‐cortical connections. This pattern of projection was consistent from one visual area to another. Pyramidal cells appeared to be the source of cortico‐geniculate, cortico‐collicular and cortico‐cortical projections. The proportion of cells within a layer that terminated in a given site varied from layer to layer: apparently all of the large pyramids in layer V had terminals in the superior colliculus, about half of the pyramids in layer VI had terminals in the lateral geniculate nucleus, while only a small proportion of the pyramids in layers II and III had terminals in any single cortical area. The results indicated a remarkable specificity in the projections of the cortical layers.
Corticosteroid-associated Osteonecrosis: A Rare, but Serious, Complication in Uveitis

Abstract Purpose: To examine the incidence and prevalence of osteonecrosis in uveitis patients. Methods: An electronic medical record database search was conducted to identify uveitis patients with osteonecrosis and the number at risk for corticosteroid-related osteonecrosis from 2003 to 2012. The clinical and ophthalmologic features of the uveitis patients with osteonecrosis were assessed with retrospective chart reviews. Results: Six uveitis patients with osteonecrosis were identified, comprising a prevalence of 1.5%. The incidence density was 0.19 per 100 person-years of follow-up. The uveitides included sarcoidosis, sympathetic ophthalmia, idiopathic retinal vasculitis, idiopathic chronic anterior and intermediate uveitis, Vogt-Koyanagi Harada disease, and Cogan syndrome. The duration of systemic corticosteroid treatment ranged from 6 weeks to 6 years. The potential systemic risk factors were Raynaud phenomenon, antiphospholipid and autoantibodies, sickle cell trait, and thalassemia. Conclusions: Although osteonecrosis appears to be a rare complication among uveitis patients, physicians should strive to minimize systemic corticosteroid use when appropriate. A higher level of suspicion for osteonecrosis may be warranted in patients with additional systemic risk factors.
Protein secondary structure prediction with context convolutional neural network

Protein secondary structure (SS) prediction is important for studying protein structure and function. Both traditional machine learning methods and deep learning neural networks have been utilized and great progress has been achieved in approaching the theoretical limit. Convolutional and recurrent neural networks are two major types of deep leaning architectures with comparable prediction accuracy but different training procedures to achieve optimal performance. We are interested in seeking novel architectural style with competitive performance and in understanding performance of different architectures with similar training procedures. Results We constructed a context convolutional neural network (Contextnet) and compared its performance with popular models (e.g. convolutional neural network, recurrent neural network, conditional neural fields …) under similar training procedures on Jpred dataset. the Contextnet was proven to be highly competitive. Additionally, we retrained the network with the Cullpdb data set and compared with Jpred, ReportX and Spider3 server, the Contextnet was found to be more accurate on CASP13 dataset. Training procedures were found to have significant impact on the accuracy of the Contextnet. Availability The full source code and dataset have been uploaded at https://github.com/qzlshy/second_structure_model and https://github.com/qzlshy/ss_pssm_hhm. Contact tianpu@jlu.edu. cn
Learning Mechanism of Automated Negotiation in E-commerce

Aiming at the shortcoming of current automated negotiation systems, this paper applied machine learning to bilateral automated negotiation. It mainly researched learning mechanism of automated negotiation in e-commerce. It improved traditional Q-learning and designed dynamic Q-learning algorithm. This algorithm estimated Q value according to environment state and the action of both agents, furthermore, recency-based exploration bonus were embedded. The paper applied Bayesian learning to negotiation strategy of automated negotiation, and designed the belief strategy based on Bayesian. Finally, this paper did experiments on learning mechanism and dynamic Q-learning algorithm. The results show that learning mechanism can improve efficiency of automated negotiation and dynamic Q-learning algorithm is efficient
Immunological diagnosis of childhood coeliac disease: comparison between antigliadin, antireticulin and antiendomysial antibodies

The immunological markers proposed to supplement intestinal biopsy for the diagnosis of coeliac disease are antigliadin, antireticulin and antiendomysial antibodies. These antibodies have been studied separately or compared as pairs, but no prospective comparison of all three antibodies in childhood coeliac disease exists. Thirty‐four confirmed coeliacs were compared with nine non‐coeliacs with pathological small intestines, and 32 children with a normal intestinal histology. Sera were examined for IgG‐ and IgA‐antigliadin antibodies (AGA) by ELISA, and for IgA‐antireticulin antibodies (ARA) and IgA endomysial antibodies (EMA) by indirect immunofluorescence. In active coeliac disease, IgA‐EMA was the most sensitive (97%), while IgA‐AGA the least sensitive antibody (52%). The specificity of IgA‐AGA, IgG‐AGA, IgA‐ARA, IgA‐EMA was 95%, 92%, 100% and 98%, respectively. Positive predicted values of ARA and EMA were comparable (97‐100%), while EMA had the highest negative predicted value (98%). Compared with IgG‐AGA, IgA‐EMA titres better reflected variations in dietary gluten, and correlated best with intestinal pathology. Compared with AGA and ARA sensitivity, specificity and predictive values, EMA is the most reliable serological marker for the diagnosis of coeliac disease. It reflects dietary changes in gluten and correlates best with intestinal histopathology. Therefore, it should be considered the best of the three serological tests available for childhood coeliac disease.
Towards Economical E-Learning Educational Environments for Physically Challenged Students

The World Health Organization defines Disability as follows: "Disabilities is an umbrella term, covering impairments, activity limitations, and participation restrictions. Impairment is a problem in body function or structure; an activity limitation is a difficulty encountered by an individual in executing a task or action; while a participation restriction is a problem experienced by an individual in involvement in life situations. Thus disability is a complex phenomenon, reflecting an interaction between features of a person’s body and features of the society in which he or she lives[1]. ” Disabilities could be natural or could happen due to accidents. Technology could be used to create new software/hardware tools to help the disabled to participate in a creative collaborative educational environment. In this chapter, we introduce two economically feasible solutions to aid physically challenged young students. They want they do (TWTD) is a simple system to help young students with hand disabilities interact with computers using web-camera and set of markers. The solution has been tested in some local schools and the results are promising [9]. Section 3 will introduce more details about version 2 of TWTD. Autistic Touchless Board (ATB) is a system to help autistic children interact with computers with their hands. The system teaches autistic kids basic math and skills by projecting the problems on any surface (walls could be used) and the students interact by pointing to the wall without the need for extra tools. Section 4 will introduce more details about the design of ATB. The rest of the chapter will be organized as follows:  Section 2 will include the frameworks used to develop the e-learning environments.  Sections 3,4 will include the two main developed environments. Each one will include the following points:  Problem  Solution
Influence of cusp coverage on the fracture resistance of premolars with endodontic access cavities.

AIM To assess the influence of cusp reduction and coverage with composite resin on the fracture resistance of premolars with prepared access cavities. METHODOLOGY Endodontic access cavities were prepared in 60 premolar teeth that were divided into four test groups: R1, R2, R3 and NR (n=15). In all test groups, MOD cavities were prepared and extended towards one of the cusps. The remaining cusp-wall thickness was: 1-1.5 mm in R1, 1.5-2 mm in R2 and 2-3 mm in both R3 and NR groups. In addition, in group R1, R2 and R3 the same cusp was reduced in height to 3.5 mm. Cuspal coverage and MOD restorations were performed using composite resin. Ten intact premolars served as positive controls and another ten MOD-prepared unrestored premolars as negative controls. Teeth were submitted to cyclic fatigue of 1.2 million cycles. A compressive load was applied 30° to the long axis of the teeth until fracture. Fracture loads were recorded and the means and the Confidence Intervals were compared. RESULTS The mean fracture resistance of each of the cusp-reduced groups R1, R2 and R3 (603, 712 and 697 N, respectively) was significantly higher than the non-reduced cusp group (305 N) and was comparable to the intact-premolar group (653 N). CONCLUSIONS Cusp reduction and coverage with composite resin significantly increased the fracture resistance of premolar teeth with MOD and endodontic access cavities.
Evolutionary rates for multivariate traits: the role of selection and genetic variation

A fundamental question in evolutionary biology is the relative importance of selection and genetic architecture in determining evolutionary rates. Adaptive evolution can be described by the multivariate breeders’ equation , which predicts evolutionary change for a suite of phenotypic traits as a product of directional selection acting on them (β) and the genetic variance-covariance matrix for those traits (G). Despite being empirically challenging to estimate, there are enough published estimates of G and β to allow for synthesis of general patterns across species. We use published estimates to test the hypotheses that there are systematic differences in the rate of evolution among trait types, and that these differences are in part due to genetic architecture. We find evidence some evidence that sexually selected traits exhibit faster rates of evolution compared to life-history or morphological traits. This difference does not appear to be related to stronger selection on sexually selected traits. Using numerous proposed approaches to quantifying the shape, size and structure of G we examine how these parameters relate to one another, and how they vary among taxonomic and trait groupings. Despite considerable variation, they do not explain the observed differences in evolutionary rates.
Driven inertial waves in spherical Couette flow.

Dynamo action in the cores of planets and stars gives rise to their magnetic fields. We explore spherical Couette flows in liquid sodium as a laboratory model of the Earth’s core. Below, we image various spatiotemporal magnetic-field modes present in spherical Couette flows. Our apparatus is comprised of two independently driven rotating spheres, radii 20 and 60 cm, with sodium filling the gap between them Fig. 1 . We apply a B0=50 G axial magnetic field from external magnets and image the resulting induced magnetic field. As the Lundquist number S= B0l * 2 0 −1/2 where l is a characteristic length scale, is the magnetic diffusivity, and is the density is small S=0.7 , the magnetic field is a passive probe of the internal flows. Data from an array of 21 Hall probes along a meridian M1. M21 , plus four more distributed along the equator E1. E4 , are used to characterize the induced magnetic field exiting the outer sphere. We have projected the resulting data onto a basis of spherical harmonics and used that projection to produce the magneticfield images shown Fig. 2 . Patterns of Coriolis-restored inertial waves are present when the Ekman number, E = / 2 ol where is the kinematic viscosity and o is the angular frequency of the outer sphere , is small, and they depend on the rotation rate ratio of the inner and outer spheres i / o. All data shown here are for fixed o =30 Hz E=1.2 10−8 . The spectrogram at the left of Fig. 2 shows the frequency content of a time series of a single equatorial probe. These wave modes are likely to occur in the Earth’s outer core, but would largely be masked from view by the mantle. FIG. 1. Experimental setup.