Miracle-dz/UniFAR-FTUs huggingface dataset:
EdeepSADPr: an extensive deep-learning architecture for prediction of the in situ crosstalks of serine phosphorylation and ADP-ribosylation

The in situ post-translational modification (PTM) crosstalk refers to the interactions between different types of PTMs that occur on the same residue site of a protein. The crosstalk sites generally have different characteristics from those with the single PTM type. Studies targeting the latter’s features have been widely conducted, while studies on the former’s characteristics are rare. For example, the characteristics of serine phosphorylation (pS) and serine ADP-ribosylation (SADPr) have been investigated, whereas those of their in situ crosstalks (pSADPr) are unknown. In this study, we collected 3,250 human pSADPr, 7,520 SADPr, 151,227 pS and 80,096 unmodified serine sites and explored the features of the pSADPr sites. We found that the characteristics of pSADPr sites are more similar to those of SADPr compared to pS or unmodified serine sites. Moreover, the crosstalk sites are likely to be phosphorylated by some kinase families (e.g., AGC, CAMK, STE and TKL) rather than others (e.g., CK1 and CMGC). Additionally, we constructed three classifiers to predict pSADPr sites from the pS dataset, the SADPr dataset and the protein sequences separately. We built and evaluated five deep-learning classifiers in ten-fold cross-validation and independent test datasets. We also used the classifiers as base classifiers to develop a few stacking-based ensemble classifiers to improve performance. The best classifiers had the AUC values of 0.700, 0.914 and 0.954 for recognizing pSADPr sites from the SADPr, pS and unmodified serine sites, respectively. The lowest prediction accuracy was achieved by separating pSADPr and SADPr sites, which is consistent with the observation that pSADPr’s characteristics are more similar to those of SADPr than the rest. Finally, we developed an online tool for extensively predicting human pSADPr sites based on the CNNOH classifier, dubbed EdeepSADPr. It is freely available through http://edeepsadpr.bioinfogo. org/. We expect our investigation will promote a comprehensive understanding of crosstalks.
Altitudinal gradient drives significant changes in soil physico-chemical and eco-physiological properties of Rhododendron anthopogon: a case study from Himalaya

The best natural laboratories for studying the ecological responses of plants are high-altitude areas like the Himalaya, where many gradients coexist on a relatively small spatial scale. Here, we investigate the effect of soil physico-chemical and eco-physiological properties on the broadleaf evergreen woody shrub Rhododendron anthopogon D.Don along an altitudinal gradient in the Kashmir Himalaya. We collected leaf and soil samples for eco-physiological and soil physico-chemical analysis, respectively, at five different sites along an altitudinal gradient (3,220–3,908 m). Our results demonstrate a significant difference between soil physico-chemical and eco-physiological parameters along the altitudinal gradient. A significant correlation was observed between different studied parameters and altitude. Principal component analysis of studied soil physico-chemical and eco-physiological parameters revealed that all the sites were grouped into four clusters according to altitude, suggesting a more pronounced effect of altitude. Our findings showed that soil infiltration capacity increased with altitude, which would be helpful for the growth and development of R. anthopogon. We also observed significant variations in eco-physiological parameters, demonstrating their critical involvement in adapting R. anthopogon to the harsh environment of the alpine regions of Kashmir Himalaya. Therefore, the present study adds to our understanding that R. anthopogon has sufficient soil physico-chemical and eco-physiological plasticity, which should be favorable for its survival in future climates, offering an adaptive advantage and expanding its range shortly.
A prognostic model based on gene expression parameters predicts a better response to bortezomib-containing immunochemotherapy in diffuse large B-cell lymphoma

Diffuse Large B-cell Lymphoma (DLBCL) is the most common type of aggressive lymphoma. Approximately 60% of fit patients achieve curation with immunochemotherapy, but the remaining patients relapse or have refractory disease, which predicts a short survival. Traditionally, risk stratification in DLBCL has been based on scores that combine clinical variables. Other methodologies have been developed based on the identification of novel molecular features, such as mutational profiles and gene expression signatures. Recently, we developed the LymForest-25 profile, which provides a personalized survival risk prediction based on the integration of transcriptomic and clinical features using an artificial intelligence system. In the present report, we studied the relationship between the molecular variables included in LymForest-25 in the context of the data released by the REMoDL-B trial, which evaluated the addition of bortezomib to the standard treatment (R-CHOP) in the upfront setting of DLBCL. For this, we retrained the machine learning model of survival on the group of patients treated with R-CHOP (N=469) and then made survival predictions for those patients treated with bortezomib plus R-CHOP (N=459). According to these results, the RB-CHOP scheme achieved a 30% reduction in the risk of progression or death for the 50% of DLBCL patients at higher molecular risk (p-value 0.03), potentially expanding the effectiveness of this treatment to a wider patient population as compared with other previously defined risk groups.
Smile with diabetes: reflections on illness perception and diabetes management behaviors of adolescents in private health care in South Africa

Background The association between illness perception and diabetes management has been well established in adults but is not clearly understood for adolescents. This article reflects on qualitative findings on illness perception from the perspective of adolescents, and suggests future research to operationalize findings. Methods Qualitative document analysis was conducted on four research projects forming part of the Smile with Diabetes project, which aims to investigate psychosocial variables in diabetes management, including illness perception, within the adolescent and youth populations. Thematic analysis was used to derive four themes from the qualitative and review studies examined in the document analysis. Results The voices of the adolescents were evident as four prominent themes: 1) living with diabetes leads to a sense of being different; 2) integration of diabetes into identity is critical, but difficult to achieve; 3) fear of potential negative consequences motivates adherence to treatment; 4) diabetes management is difficult, but possible. Conclusion The findings not only confirmed the importance of illness perception in the management of diabetes by adolescents, but also indicate that illness perceptions should be investigated from a developmental perspective, specifically taking identity development into consideration in this group. Adolescents should be made aware of how their thinking about diabetes and its management affects their experience of living with diabetes and its future management. This study further contributes to the literature by focusing on the patient’s voice in understanding living with a chronic condition, and reassures that positive outcomes are possible when living with a chronic condition such as diabetes.
Formulation and validation of a baseline prognostic score for osteosarcoma treated uniformly with a non-high dose methotrexate-based protocol from a low middle income healthcare setting: a single centre analysis of 594 patients

Introduction The outcomes of osteosarcoma in low middle income countries (LMICs) are different due to patients presenting in advanced stages, resource constraints and the use of non-high-dose-methotrexate (HDMTX)-based regimens. This study derived and validated a prognostic score for osteosarcoma that integrates biologic and social factors and is tailored for patients from an LMIC setting using a non-HDMTX-based protocol. Materials and methods A retrospective study including osteosarcoma patients enrolled for treatment at a single tertiary care centre in India between 2003-19 was conducted. Baseline biologic and social characteristics were extracted from medical records and survival outcomes were noted. The cohort was randomised into a derivation and validation cohort. Multivariable Cox regression was used to identify baseline characteristics that were independently prognostic for survival outcomes in the derivation cohort. A score was derived from the prognostic factors identified in the derivation cohort and further validated in the validation cohort with estimation of its predictive ability. Results 594 patients with osteosarcoma were eligible for inclusion in the study. Around one-third of the cohort had metastatic disease with 59% of the patients residing in rural areas. The presence of metastases at baseline (HR 3.39; p<0.001; score=3), elevated serum alkaline phosphatase (SAP) >450 IU/L (HR 1.57; p=0.001; score=1) and baseline tumour size > 10 cm (HR 1.68; p<0.001; score=1) were identified to be independent factors predicting inferior event free survival (EFS) and were included in development of the prognostic score. Patients were categorized as low risk (score 0), intermediate risk (score 1-3) and high risk (4-5). Harrell’s c-indices for the score were 0.682, 0.608 and 0.657 respectively for EFS in the derivation, validation and whole cohort respectively. The timed AUC of ROC was 0.67 for predicting 18-month EFS in the derivation, validation and whole cohorts while that for 36-month EFS were 0.68, 0.66 and 0.68 respectively. Conclusions The study describes the outcomes among osteosarcoma patients from an LMIC treated uniformly with a non-HDMTX-based protocol. Tumor size, baseline metastases and SAP were prognostic factors used to derive a score with good predictive value for survival outcomes. Social factors did not emerge as determinants of survival.
Greybody Factors Hawking Radiation in Disguise

This master’s thesis deals with greybody factors of static and spherically symmetric black holes in asymptotically flat spacetimes, with emphasis on the high frequency limit. The first goal is to provide a pedagogical and thorough review of some recent developments in the study of these objects in a semiclassical context. The second goal is to motivate further investigation in this subject as a possible way to gain a better understanding of quantum gravity. We first review an important string theoretical result in the low frequency regime, which gave new insight into the microscopics of black holes. To perform the computations at high frequency, we use the monodromy technique, first introduced in this context by Motl and Neitzke. The results we obtain in this regime are highly suggestive and drawing on the results at low frequency, it has been suggested that they might be telling us something new about the quantum structure of black holes. We conclude by presenting an attempt of using the monodromy technique to compute the greybody factor at high frequency for a stringy black hole. The hope is that the result in this case might be easier to realize in the context of string theory.
Permanent of the product of doubly stochastic matrices

If A = [aij] is an n × n matrix, the permanent of A is the scalar valued function of A defined by where the summation extends over all permutations (i1, i2, …, in) of the integers 1, 2, …, n. If we assume that A is a non-negative matrix (that is, that A has non-negative entries) then we come upon an extremely interesting situation. Much work has been done in finding significant upper bounds for the permanent and permanental minors of A (see, e.g. (2, 4–7) in (5) an excellent bibliography is given). If B = [bij] is another n × n non-negative matrix, then we may form the product AB and consider the permanent of this matrix. Unlike the determinant, the permanent is not a multiplicative function. In our circumstances here, however, it is easy to verify and indeed a proof was written down in (1) that
A new method of solving Oseen’s equations and its application to the flow past an inclined elliptic cylinder

In this paper is developed a general method of solving Oseen’s linearized equations for a two-dimensional steady flow of a viscous fluid past an arbitrary cylindrical body. The method is based on the fact that the velocity in the neighbourhood of the cylinder can be generally expressed in terms of a pair of analytic functions, the determination of which from the appropriate boundary condition can be effected by successive approximations in powers of the Reynolds number, R. The method enables one to obtain the velocity distribution near the cylinder and the lift and drag acting on it in the form of power series in R, without recourse to manipulation of higher transcendental functions such as Bessel and Mathieu functions for circular and elliptic cylinders, respectively. As an example of the application of the method, the uniform flow past an elliptic cylinder at an arbitrary angle of incidence is considered. Analytical expressions for the lift and drag coefficients are obtained, which are correct to the order of R, the lowest order terms being O(R-1) and numerical calculations are carried out for the thickness ratio t = 0, 0.1, 0.5, 1 and the Reynolds number R = 0.1, 1. It is found that drag increases slightly with increase of either thickness ratio or angle of incidence, and that lift decreases with increase of thickness ratio while, as a function of the angle of incidence, it has a maximum at about 45°.
Self-Complementary Arc-Transitive Graphs and Their Imposters

This thesis explores two infinite families of self-complementary arc transitive graphs: the familiar Paley graphs and the newly discovered Peisert graphs. After studying both families, we examine a result of Peisert which proves the Paley and Peisert graphs are the only self-complementary arc transitive graphs other than one exceptional graph on 232 vertices. Then we consider other families of graphs which share many properties with the Paley and Peisert graphs. In particular, we construct an infinite family of self-complementary strongly regular graphs from affine planes. We also investigate the pseudo-Paley graphs of Weng, Qiu, Wang, and Xiang. Finally, we prove a lower bound on the number of maximal cliques of certain pseudoPaley graphs, thereby distinguishing them from Paley graphs of the same order.
Students Mathematization Process of the Concept of Slope within the Realistic Mathematics Education

The aim of this study is to analyze eight grade students’ mathematizing processes of the concept of slope in light of the teaching process designed based on Realistic Mathematics Education. Participants of this design based research study were chosen via purposeful sampling in accordance with results of an open-ended test intended for prerequisite information before design teaching-learning environment. Survey data was acquired from open-ended test, researcher log, individual and group study papers and clinical interviews. Contexts, which provide opportunities to reflect preliminary conceptions of slope to teaching process are revealed. Conceptualization process of slope as ratio started with the need to be base of informal linear constant. Then it develops with the need of measurement of slope. Students reinvent that the slope is also an algebraic ratio by reflecting geometric ratio representation to coordinate plane. Designed teaching in this study was revealed that mathematization is important in transition among representations. Development of right triangle model occurred in three phases: (i) a context-dependent interpretive tool, (ii) a physical tool used to calculate the slope, (iii) a cognitive tool that that is no longer needed to be represented physically.
Postpartum Preeclampsia

Postpartum preeclampsia has not received the needed attention that preeclampsia has. It is the lesser-known hypertensive disorder but can be just as life-threatening as eclampsia. Because of the scarcity of qualitative research on postpartum preeclampsia, the purpose of this study was to help fill this gap by exploring personal experiences of this dangerous complication as described in online blogs. Using Google search engine, 25 stories of postpartum preeclampsia were located. Krippendorff's content analysis for qualitative data was the research design used. Five themes were identified: (1) Not even on my radar as a new mom, (2) Bombarded with physical and emotional symptoms, (3) Life-threatening situation: Dismissed or misdiagnosed, (4) Heartbroken: Separation from my newborn, and (5) Trust your instincts and advocate for yourself. Advanced practice nurses and other health care providers need to be on alert for postpartum preeclampsia when a woman, who recently gave birth, presents at the emergency department.
Scenario-Based Model Checking of Declarative Process Models

: Modeling processes with declarative process models , i.e. sets of constraints which have to be satisfied throughout the whole process execution, allows for a great degree of flexibility in process execution. However, having a process specified by means of symbolic, textual or formal constraints comes along with the problem that it is often hard for humans to understand complicated interactions of constraints and overlook the entire process model without unintentionally neglecting important process details. Caused by these reasons, standard questions regarding process models, e.g. ”Can a running process instance still be completed successfully? ” , can often only be answered with great computational and temporal effort or even not at all. In this paper we present an efficient scenario-based approach for declarative process models, which supports process modelers in checking process models for important and common scenarios which regularly occur when modeling declarative processes. We implement our approach and show that the solutions for the scenarios can be computed within milliseconds even for real-life event logs. Furthermore, a user study conducted demonstrates that the error rate in understanding declarative process models is enormously reduced by using our implementation.
Efficacy of photodynamic therapy using UVB radiation-emitting novel phosphor material for non-surgical treatment of psoriasis

Ultraviolet (UV) light is the key to treat various skin conditions effectively. Commercial UV lamps emit a broad spectrum (width > 100 nm) and are widely used to treat skin diseases. Psoriasis is a non-contagious long-term skin infection that affects many people worldwide. Only a small part of the UV light spectrum is required for skin rejuvenation, which corresponds to action spectrum of psoriasis. However, the use of broadband emitting commercial UV light leads to side effects such as skin tanning, erythema, etc. To avoid this issue, a series of UV emitting Ca_2MgSi_2O_7:Gd^3+ phosphors that have a specific narrow wavelength range were prepared for the first time with promising results in the field of dermatology. The optimized Ca_2-xMgSi_2O_7:xGd^3+ phosphor had an intensity comparable to commercial LaPO_4:Ce^3+ phosphor (UVB-315), making the developed phosphor a promising option for the effective treatment of psoriasis in fewer lesions with minimal risk of erythema. Graphical abstract
The possibility of detection of finite temperature stripe ordering in 2D spinless Falicov–Kimball model

This paper announces a possibility of detection of finite-temperature stripe ordering in the two-dimensional Falicov–Kimball model at half-filling by extensive Monte Carlo simulations. Moreover, the tools to study orderings and to detect phase transition temperatures are presented. The use of Binder's cumulant is supplemented by finite-size magnetization profiles not analyzed previously in this context. Continuous character of phase transitions is announced. Analyses proving the existence of more complicated phases of finite-temperature stripe ordering than the checkerboard one conclude the paper.
Using different levels of coated calcium sodium butyrate in the diet of quail on growth performance, duodenal histomorphology, and some biochemical parameters

: The aim of this study was to determine growth performance, duodenal histomorphology, and some biochemical parameters in quails’ diets containing coated calcium sodium butyrate (CSB). One hundred sixty 1-day-old Japanese quails were arranged into four trial groups consisting of 5 replicates with eight chicks per replicate. One group was formed as a control group without CSB, and the other experimental groups were formed by adding CSB at the level of 0.06% (CSB - 1), 0.08% (CSB - 2), and 0.1% (CSB - 3). All diets were prepared isonitrogenically and isocalorically, with 24% CP and 3000 kcal/kg ME content. The trial was completed at 35 days. At the end of the study, the highest body weight (BW) and body weight gain increase in the CSB - 3 group, which was supplemented with 0.1% CSB. The feed conversion ratio was to determine that ad a linear and quadratic improvement in the CSB - 3 group. The highest villi height was found in the CSB - 2 group, the highest villi: crypt ratio was found in the CSB - 3 group, and the lowest crypt depth was found in the CSB - 3 group. Serum aspartate aminotransferase, alanine aminotransferase, low-density lipoprotein, high-density lipoprotein, and triglyceride values decreased in the experimental groups compared to the control group. However, Ca and P values increased in the control group. No differences were noticed in carcass yield and visceral weights of the experimental groups.
Radiative and Microphysical Characteristics of Deep Convective Systems in the Tropical Western Pacific

Abstract The radiative and microphysical characteristics of 17 precipitating systems observed by the Tropical Rainfall Measuring Mission (TRMM) satellite over Manus, Papua New Guinea, and Nauru Island are modeled. These cases represent both deep and midlevel convection. Reflectivity data from the TRMM precipitation radar and Geostationary Meteorological Satellite infrared radiometer measurements are used to parameterize the three-dimensional cloud microphysics of each precipitating cloud system. These parameterized cloud properties are used as input for a two-stream radiative transfer model. Comparisons with measurements of broadband radiative fluxes at the top of atmosphere and the surface show agreement to within 20%. In cases in which the convective available potential energy (CAPE) is large, deep convective clouds with extended anvil decks form, containing layers of ice crystals that are too small to be detected by the TRMM radar but have a large optical thickness. This results in maximum shortwave he.
Revision needed? A social constructionist perspective on measurement scales for assessing gender role stereotypes in entrepreneurship

This article compares contemporary views of who and what constitutes entrepreneurship with dimensions captured in established scales for determining gender role stereotypes associated with entrepreneurship. In so doing, we respond to ongoing debates about the timeliness, contextualisation and predetermination of scales, such as Schein’s Descriptive Index (SDI), Bem’s Sex Role Inventory (BSRI) and the Personal Attribute Questionnaire (PAQ). Our empirical study consists of 422 descriptions of an entrepreneurial ideal provided by a sample of young adults, which we analysed using quantitative content analysis. The comparison between participants’ perceptions and the items captured in the gender role stereotype scales shows only a partial overlap. Although masculine qualities are mentioned, we find various androgynous (e.g., passion, team player, willingness to learn) qualities of entrepreneurs not covered in SDI, BSRI or PAQ. Based upon this, we can derive several recommendations on how established scales can be revised through future research.