Miracle-dz/UniFAR-FTUs huggingface dataset:
An Accurate de novo Algorithm for Glycan Topology Determination from Mass Spectra

Determining the glycan topology automatically from mass spectra represents a great challenge. Existing methods fall into approximate and exact ones. The former including greedy and heuristic ones can reduce the computational complexity, but suffer from information lost in the procedure of glycan interpretation. The latter including dynamic programming and exhaustive enumeration are much slower than the former. In the past years, nearly all emerging methods adopted a tree structure to represent a glycan. They share such problems as repetitive peak counting in reconstructing a candidate structure. Besides, tree-based glycan representation methods often have to give different computational formulas for binary and ternary glycans. We propose a new directed acyclic graph structure for glycan representation. Based on it, this work develops a de novo algorithm to accurately reconstruct the tree structure iteratively from mass spectra with logical constraints and some known biosynthesis rules, by a single computational formula. The experiments on multiple complex glycans extracted from human serum show that the proposed algorithm can achieve higher accuracy to determine a glycan topology than prior methods without increasing computational burden.
Variable-Frame Level-n Theory

Abstract We develop a boundedly rational version of variable frame theory by merging the variable-frame concept with level- n theory. Variable frame theory assumes that a player's options are determined by a set of attributes (her “frame”), which induce a partition of the action set. Schelling competence emerges by combining frame-induced options with unbounded rationality and with payoff-dominance and symmetry disqualification. The weak empirical evidence for these assumptions motivates variable frame level- n theory, which predicts the Schelling competence by combining a nonrational level-0 tendency with reasoning by higher-level players. Journal of Economic Literature Classification Numbers: B41, C70.
The ability of high school students’ critical thinking in solving trigonometric problems

Critical Thinking has been one of the tools used in our daily life’s to deal with the challenges for survival. Developing critical thinking abilities is something which is very important in the world of education today. Problem solving can support increased critical thinking abilities This study aims at describing the students’ critical thinking skills in solving Trigonometry problems. Critical thinking ability in this research employs an indicator which consists of Focus, Reason, Inference, Situation, Clarity, and Overview. The type of this research is descriptive research with qualitative approach. The research subjects consist of 3 students, i.e. high-ability student (ST), medium (SS) and low (SR). The results of this study indicate that there are 5 indicators that can be achieved by the high-ability student (ST) namely Focus, Reason, Situation, Clarity, and Overview. Meanwhile the medium students are capable of achieving 2 indicators only, namely Focus and Reason and low ability student achieves 1 indicator of critical thinking ability, namely Reason.
Sizing up the nucleus: nuclear shape, size and nuclear-envelope assembly

The nucleus is one of the most prominent cellular organelles, yet surprisingly little is known about how it is formed, what determines its shape and what defines its size. As the nuclear envelope (NE) disassembles in each and every cell cycle in metazoans, the process of rebuilding the nucleus is crucial for proper development and cell proliferation. In this Commentary, we summarize what is known about the regulation of nuclear shape and size, and highlight recent findings that shed light on the process of building a nucleus, including new discoveries related to NE assembly and the relationship between the NE and the endoplasmic reticulum (ER). Throughout our discussion, we note interesting aspects of nuclear structure that have yet to be resolved. Finally, we present an idea – which we refer to as `the limited flat membrane hypothesis' – to explain the formation of a single nucleus that encompasses of all of the cell's chromosomes following mitosis.
Abnormality of EEG Alpha Asymmetry Adolescent Suicide Attempters in Female

Abnormal electroencephalographic (EEG) activity has been associated with various psychiatric disorders and behaviors, including depression, suicide, and aggression. We examined quantitative resting EEG in Hispanic female adolescent suicide attempters and matched normal controls. Computerized EEG measures were recorded at 11 scalp sites during eyes open and eyes closed periods from 16 suicide attempters and 22 normal controls. Suicide attempters differed from normal controls in alpha asymmetry. Normal adolescents had greater alpha (less activation) over right than left hemisphere, whereas suicidal adolescents had a nonsignificant asymmetry in the opposite direction. Nondepressed attempters were distinguished from depressed attempters in that they accounted for the preponderance of abnormal asymmetry, particularly in posterior regions. Alpha asymmetry over posterior regions was related to ratings of suicidal intent, but not depression severity. The alpha asymmetry in suicidal adolescents resembled that seen for depressed adults in its abnormal direction, but not in its regional distribution. Findings for suicidal adolescents are discussed in terms of a hypothesis of reduced left posterior activation, which is not related to depression but to suicidal or aggressive behavior.
Objective Measurement of Physical Activity and Sedentary Behavior Among US Adults Aged 60 Years or Older

Introduction Estimates of objectively measured physical activity among older adults differ depending on the cut points used to define intensity. Our objective was to assess 1) moderate to vigorous physical activity (MVPA), exploring differences in prevalence depending on the cut point used, and 2) sedentary behavior, among US adults aged 60 years or older. Methods We used the most recently available accelerometer data (2003-2004 and 2005-2006) from the National Health and Nutrition Examination Survey. The sample included 2,630 adults aged 60 or older who wore an ActiGraph accelerometer for 1 week. We defined MVPA using 4 cut points (≥500, ≥1,000, ≥1,500, and ≥2,000 counts/min) and sedentary behavior as fewer than 100 counts per minute. All estimates were weighted to reflect the US population. Results The overall average counts per minute was 216. Mean MVPA ranged from 10.8 minutes per day (based on 2,000 counts/min) to 106.8 minutes per day (based on 500 counts/min). Regardless of the cut point used, MVPA was lower with each successive age group (60-69, 70-79, and ≥80) and higher among men than women. At any cut point, MVPA was highest for Hispanics and "other" racial/ethnic groups, followed by non-Hispanic whites and non-Hispanic blacks. The average time spent in sedentary behavior was 8.5 hours per day. The amount of sedentary time was greater among participants who were aged 80 or older compared to younger groups and among men compared to women. Conclusion MVPA estimates vary among adults aged 60 or older, depending on the cut point chosen, and most of their time is spent in sedentary behaviors. These considerations and the data presented suggest more research is necessary to identify the appropriate method of setting accelerometer cut points for MVPA in older adults.
Are there prospects for future economic integration among Muslim countries? Evidence from selected OIC countries

Since mid-1980s, trade has been one of the main agenda among the Organization of Islamic Conference (OIC) member countries as a means towards achieving higher economic development. January 1st, 2009 has been declared as the target date for the establishment of the Trade Preferential System among the OIC countries, by which date intra-trade should be increased to 20%. Malaysia, which is considered to be one of the more successful economies among the OIC countries, is expected to play a pivotal role in enhancing intra-trade and ensuring that the targets are achieved. This paper investigates the degree of intra-trade activities among six OIC members, namely Egypt, Jordan, Malaysia, Saudi Arabia, Syria and Oman. It analyzes the trade structure of these OIC members utilizing “revealed comparative advantage” indices, “trade concentration”, and “trade competition” profiles. The findings show only small potentials for higher intra-OIC trade, generally in chemicals and materials, food and live animals, manufactured goods, and machinery and transport equipment. This indicates that much greater efforts need to be undertaken by OIC countries to prepare themselves for the establishment of an Islamic Common Market.
How Exercise May Amend Metabolic Disturbances in Diabetic Cardiomyopathy

Abstract Significance: Over-nutrition and sedentary lifestyle has led to a worldwide increase in obesity, insulin resistance, and type 2 diabetes (T2D) associated with an increased risk of development of cardiovascular disorders. Diabetic cardiomyopathy, independent of hypertension or coronary disease, is induced by a range of systemic changes and may through multiple processes result in functional and structural cardiac derangements. The pathogenesis of this cardiomyopathy is complex and multifactorial, and it will eventually lead to reduced cardiac working capacity and increased susceptibility to ischemic injury. Recent Advances: Metabolic disturbances such as altered lipid handling and substrate utilization, decreased mechanical efficiency, mitochondrial dysfunction, disturbances in nonoxidative glucose pathways, and increased oxidative stress are hallmarks of diabetic cardiomyopathy. Interestingly, several of these disturbances are found to precede the development of cardiac dysfunction. Critical Issues: Exercise training is effective in the prevention and treatment of obesity and T2D. In addition to its beneficial influence on diabetes/obesity-related systemic changes, it may also amend many of the metabolic disturbances characterizing the diabetic myocardium. These changes are due to both indirect effects, exercise-mediated systemic changes, and direct effects originating from the high contractile activity of the heart during physical training. Future Directions: Revealing the molecular mechanisms behind the beneficial effects of exercise training is of considerable scientific value to generate evidence-based therapy and in the development of new treatment strategies. Antioxid. Redox Signal. 22, 1587–1605.
ANALYSIS OF FAMILIAR BUSINESSES AND THEIR DIFFICULTIES IN THE PROFESSIONALIZATION PROCESS

Our study aims to identify the main difficulties faced by family and non-family managers in the process of a family business professionalization. The method applied is initially characterized as exploratory, resulting from the need to search the literature produced on this topic. Our method was the multiple case studies, with three family businesses with family and non-family managers. Information and data collection were carried out with pre-scheduled interviews with CEOs and business managers while following a semi-structured script. We applied open-ended questions, which were carried out individually, recorded and transcribed with the goal of highlighting common points in the reports of the interviewees, as well as confronting them. We analyzed the content based on the theoretical foundation carried out qualitatively. Thus, we were able to confront the theory to the firms’ reality, making it possible to reach the main goal of this study. The interviewees assigned the difficulties of the professionalization to some common factors among them, such as lack of feedback, overconfidence, miscommunication, and favoritism. These characteristics were confirmed by the interviewees. It is evident that despite the difference of each firm lifespan, the common ground is the same, and the difficulties in the process of professionalization are also similar regardless of the stage of the process.
Is pubertal timing associated with involvement in bullying in middle adolescence?

Off-time pubertal maturation is associated with mental disorders, presumably due to stress caused by deviation from peers that could also attract negative attention and result in being bullied. Stress related to off-time maturation could be acted out by involving oneself in bullying behavior. The associations between pubertal timing and involvement in bullying have so far not been a focus of research. The objective is to explore associations between off-time pubertal maturation and involvement in bullying. Cross-sectional and longitudinal associations between self-reported pubertal timing and involvement in bullying as victims and perpetrators were studied in a sample of 2070 Finnish adolescents aged 15–17 who participated in the Adolescent Mental Health Cohort Study. Internalizing (depression) and externalizing (conduct disorder) symptoms were controlled for. The adolescents were recruited to response the baseline survey in 2002–2003 (T1) and follow-up two years later (T2). In T1, response rate was 94.4% of all eligible students. The 2070 participants in T2 comprised 63.1% of the T1 participants. Early maturation among boys was cross-sectionally associated with being a bully, and late maturation with exclusion from peer group. After two years, the associations had disappeared. Among girls, no associations were detected between pubertal timing and involvement in bullying. Off-time pubertal maturation places boys at risk for involvement in bullying. The influence is transient and supports the stressful change hypothesis of pubertal timing.
The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010–2015: The Experience of Sicily and Liguria

Molecular epidemiology of influenza B virus remained poorly studied in Italy, despite representing a major contributor to seasonal epidemics. This study aimed to reconstruct the phylogenetic relationships and genetic diversity of the hemagglutinin gene sequences of 197 influenza B strains circulating in both Southern (Sicily) and Northern (Liguria) Italy between 2010 and 2015. Upper respiratory tract specimens of patients displaying symptoms of influenza-like illness were screened by real-time RT-PCR assay for the presence of influenza B virus. PCR-positive influenza B samples were further analyzed by sequencing. Neighbor-joining phylogenetic trees were constructed and the amino-acid alignments were analyzed. Phylogenetic analysis showed clusters in B/Victoria clade 1A/1B (n = 29, 14.7%), and B/Yamagata clades 2 (n = 112, 56.8%) and 3 (n = 56, 28.4%). Both influenza B lineages were found to co-circulate during the study period, although a lineage swap from B/Victoria to B/Yamagata occurred in Italy between January 2011 and January 2013. The most represented amino-acid substitutions were N116K in the 120-loop (83.9% of B/Yamagata clade 3 strains) and I146V in the 150-loop (89.6% of B/Victoria clade 1 strains). D197N in 190-helix was found in almost all viruses collected. Our findings provide further evidence to support the adoption of quadrivalent influenza vaccines in our country.
Gabor Wavelet-Based Appearance Models

There has been considerable research in the last several years based on the principles of Active Appearance Models (AAMs). AAM is a robust methodology for general image (object) descriptions that incorporates shape and texture information. In this work, we extend the basic AAMs by developing a new method for texture description for the application of human facial modeling and synthesizing. The premise is to develop a better texture based model for the face that incorporates specific facial information such as wrinkling, micro-features (e.g., moles, scares, freckles, etc.), and aging features (e.g., sagging, hollowing of checks, weight gain, etc.) This paper proposes a new improvement in texture synthesis-Gabor Wavelet-based Appearance Model. The experimental results demonstrate the potential of this approach for face-based applications.
Studies on the capacity of MIMO systems in mobile-to-mobile environment

The use of multiple input and multiple output (MIMO) antennas is a promising technique for increasing the capacity of wireless communication systems. Huge capacities are guaranteed only when channels between different transmitting and receiving antenna pairs are statistically independent. In this paper, we investigate the capacities of MIMO systems in a mobile-to-mobile environment by employing a "two ring" model which is simple extension of previous "one ring" model. With this model, we investigate the spatial correlation and information theoretic channel capacity of MIMO systems that use omni-directional antennas as well as MIMO systems with directional antennas. We show that MIMO systems with directional antennas yield good spatial decorrelation between antenna pairs even in a scarce scattering environment, while MIMO systems with omni-directional antennas suffer capacity degradation either when antennas are located closely each other, or when there is not enough multipath richness. Directional antennas guarantee the independence between different antenna pairs by not sharing scatterers, and the capacity is maximized by exploiting the independence between antenna pairs.
Adsorption in a Fixed-Bed Column and Stability of the Antibiotic Oxytetracycline Supported on Zn(II)-[2-Methylimidazolate] Frameworks in Aqueous Media

A metal-organic framework, Zn-[2-methylimidazolate] frameworks (ZIF-8), was used as adsorbent material to remove different concentrations of oxytetracycline (OTC) antibiotic in a fixed-bed column. The OTC was studied at concentrations of 10, 25 and 40 mg L-1. At 40 mg L-1, the breakthrough point was reached after approximately 10 minutes, while at 10 and 25 mg L-1 this point was reached in about 30 minutes. The highest removal rate of 60% for the 10 mg L-1 concentration was reached after 200 minutes. The highest adsorption capacity (28.3 mg g-1) was attained for 25 mg L-1 of OTC. After the adsorption process, a band shift was observed in the UV-Vis spectrum of the eluate. Additional studies were carried out to determine the cause of this band shift, involving a mass spectrometry (MS) analysis of the supernatant liquid during the process. This investigation revealed that the main route of adsorption consisted of the coordination of OTC with the metallic zinc centers of ZIF-8. The materials were characterized by thermal analysis (TA), scanning electron microscopy (SEM), powder X-ray diffraction (XRD), and infrared spectroscopy (IR) before and after adsorption, confirming the presence of OTC in the ZIF-8 and the latter’s structural stability after the adsorption process.
Homomorphisms in Graph Property Testing - A Survey

Property-testers are fast randomized algorithms for distinguishing between graphs (and other combinatorial structures) satisfying a certain property, from those that are far from satisfying it. In many cases one can design property-testers whose running time is in fact independent of the size of the input. In this paper we survey some recent results on testing graph properties. A common thread in all the results surveyed is that they rely heavily on the simple yet useful notion of graph homomorphism. We mainly focus on the combinatorial aspects of property-testing.
Police Officer Transformational Leadership: Development and Validation of a Self-reported Scale

The aim of this study is to develop and test the factorial validity of a questionnaire about police officer’s transformational leadership on the ground. Based on Bass’s (1985) transactional/transformational leadership model, Police Officers Transformational Leadership Scale is composed of 33 items rated on a Likert-type scale from (1) Completely disagree to (6) Completely agree. Respondents were 167 police officers from a large French Canadian police organization and two small police corps. The results show that a model structure with two second-order dimensions (transactional and transformational leadership), consistent with Bass’s theory (1985), provided a good fit to the data. The results suggest that this questionnaire is well suited for describing the transformational leadership of police officers.
Molecular and clinical characterization of PD-L1 expression at transcriptional level via 976 samples of brain glioma

ABSTRACT Background: PD-L1 has been widely reported as immune check points in a range of malignancies as well as some immune-originated diseases. In glioma, the role of PD-L1 remains unclear. We aimed at investigating its role at transcriptome level and relationship with clinical practice. Method and patients: In total, 976 glioma samples with transcriptome data, including 301 microarray data from Chinese Glioma Genome Atlas (CGGA project) and 675 RNAseq data from TCGA project, were enrolled into our study. Clinical and IDH mutation data were also available. R language was used as the main tool for statistical analysis and graphical work. Results: PD-L1 expression was found to be positively correlated with WHO grade of glioma. PD-L1 seemed to express more in mesenchymal subtype according to TCGA transcriptional classification scheme and may contribute as a potential marker for mesenchymal subtype in glioblastoma. Pearson correlation test indicated that PD-L1 showed robust correlation with PD1, PD-L2, and CD80 in CGGA dataset. Subsequent gene ontology analysis based on significantly correlated genes of PD-L1 revealed that PD-L1 seemed to be profoundly associated with T cell activation. To further investigate the relationship between PD-L1 expression and immune response, we selected a series of immune signatures, which were then transformed into metagenes, and found that PD-L1 expression was particularly paralleled with T-cells and macrophages-related immune response instead of B cell linage-related immune response. In line with the corresponding biological process, PD-L1 exhibited predictive value for glioma patients: Higher PD-L1 indicated significantly shorter survival, especially in glioblastoma. Conclusion: PD-L1 is upregulated in glioblastoma, and is synergistic with other check point members. Moreover, PD-L1 is significantly associated with T-cell activation and macrophage-related immune response and predicts much worse survival for patients, warranting clinical trials of PD1/PD-L1 checkpoint inhibitors for potential glioma treatment.
Optimal Stopping Analysis of a Radiation Detection System to Protect Cities from a Nuclear Terrorist Attack

We formulate and analyze an optimal stopping problem concerning a terrorist who is attempting to drive a nuclear or radiological weapon toward a target in a city center. In our model, the terrorist needs to travel through a two‐dimensional lattice containing imperfect radiation sensors at some of the nodes, and decides at each node whether to detonate the bomb or proceed. We consider five different scenarios containing various informational structures and two different sensor array topologies: the sensors are placed randomly or they form an outer wall around the periphery of the city. We find that sensors can act as a deterrent in some cases, and that the government prefers the outer wall topology unless the sensors have a very low detection probability and the budget is tight (so that they are sparsely deployed).