Miracle-dz/UniFAR-FTUs huggingface dataset:
On Measuring Social Dynamics of Online Social Media

Due to the complex nature of human behaviour and to our inability to directly measure thoughts and feelings, social psychology has long struggled for empirical grounding for its theories and models. Traditional techniques involving groups of people in controlled environments are limited to small numbers and may not be a good analogue for real social interactions in natural settings due to their controlled and artificial nature. Their application as a foundation for simulation of social processes suffers similarly. The proliferation of online social media offers new opportunities to observe social phenomena “in the wild” that have only just begun to be realised. To date, analysis of social media data has been largely focussed on specific, commercially relevant goals (such as sentiment analysis) that are of limited use to social psychology, and the dynamics critical to an understanding of social processes is rarely addressed or even present in collected data. This thesis addresses such shortfalls by: (i) presenting a novel data collection strategy and system for rich dynamic data from communities operating on Twitter; (ii) a data set encompassing longitudinal dynamic information over two and a half years from the online pro-ana (pro-anorexia) movement; and (iii) two approaches to identifying active social psychological processes in collections of online text and network metadata: an approach linking traditional psychometric studies with topic models and an algorithm combining community detection in user networks with topic models of the social media text they generate, enabling identification of community specific topic usage.
Antimicrobial resistance characteristics and fitness of Gram-negative fecal bacteria from volunteers treated with minocycline or amoxicillin

A yearlong study was performed to examine the effect of antibiotic administration on the bacterial gut flora. Gram-negative facultative anaerobic bacteria were recovered from the feces of healthy adult volunteers administered amoxicillin, minocycline or placebo, and changes determined in antimicrobial resistance (AMR) gene carriage. Seventy percent of the 1039 facultative anaerobic isolates recovered were identified by MALDI-TOF as Escherichia coli. A microarray used to determine virulence and resistance gene carriage demonstrated that AMR genes were widespread in all administration groups, with the most common resistance genes being blaTEM, dfr, strB, tet(A), and tet(B). Following amoxicillin administration, an increase in the proportion of amoxicillin resistant E. coli and a three-fold increase in the levels of blaTEM gene carriage was observed, an effect not observed in the other two treatment groups. Detection of virulence genes, including stx1A, indicated not all E. coli were innocuous commensals. Approximately 150 E. coli collected from 6 participants were selected for pulse field gel electrophoresis (PFGE), and a subset used for characterisation of plasmids and Phenotypic Microarrays (PM). PFGE indicated some E. coli clones had persisted in volunteers for up to 1 year, while others were transient. Although there were no unique characteristics associated with plasmids from persistent or transient isolates, PM assays showed transient isolates had greater adaptability to a range of antiseptic biocides and tetracycline; characteristics which were lost in some, but not all persistent isolates. This study indicates healthy individuals carry bacteria harboring resistance to a variety of antibiotics and biocides in their intestinal tract. Antibiotic administration can have a temporary effect of selecting bacteria, showing co-resistance to multiple antibiotics, some of which can persist within the gut for up to 1 year.
OBSERVATIONS ON THE FINE STRUCTURE AND CYTOCHEMISTRY OF MOUSE AND HUMAN INTERCOSTAL NEUROMUSCULAR JUNCTIONS

The fine structure of the mouse and human intercostal muscle neuromuscular junction was studied after brief fixation in a new formol-sucrose fixative. This primary formalin fixation was followed by brief postosmication in buffered 1 per cent osmium tetroxide. Muscle blocks were embedded in methacrylate or Epon 812 epoxy resin. Marked similarities between mouse and human motor end-plates were observed. Neuromuscular junctions from both mouse and human intercostal muscle showed synaptic vesicles, primary and secondary synaptic clefts, and layered differentiation of the amorphous surface material (ASM) present on the surface of the Schwann cell plasma membrane and on the muscle surface membrane in the region of the neuromuscular junction. An attempt to stain the ASM with lead was unsuccessful. Observations on thick and thin plastic-embedded sections stained by PAS after diastase digestion showed that the ASM within the subneural apparatus is PAS positive. Alcian blue stained the endoneurium and perineurium of peripheral nerve bundles and portions of the end-plates. The similarity of the PAS-positive ASM to other basement membranes described in other sites is discussed and its possible physiologic significance within the subsynaptic apparatus is considered.
The Effect of Surface Wave Propagation on Neural Responses to Vibration in Primate Glabrous Skin

Because tactile perception relies on the response of large populations of receptors distributed across the skin, we seek to characterize how a mechanical deformation of the skin at one location affects the skin at another. To this end, we introduce a novel non-contact method to characterize the surface waves produced in the skin under a variety of stimulation conditions. Specifically, we deliver vibrations to the fingertip using a vibratory actuator and measure, using a laser Doppler vibrometer, the surface waves at different distances from the locus of stimulation. First, we show that a vibration applied to the fingertip travels at least the length of the finger and that the rate at which it decays is dependent on stimulus frequency. Furthermore, the resonant frequency of the skin matches the frequency at which a subpopulation of afferents, namely Pacinian afferents, is most sensitive. We show that this skin resonance can lead to a two-fold increase in the strength of the response of a simulated afferent population. Second, the rate at which vibrations propagate across the skin is dependent on the stimulus frequency and plateaus at 7 m/s. The resulting delay in neural activation across locations does not substantially blur the temporal patterning in simulated populations of afferents for frequencies less than 200 Hz, which has important implications about how vibratory frequency is encoded in the responses of somatosensory neurons. Third, we show that, despite the dependence of decay rate and propagation speed on frequency, the waveform of a complex vibration is well preserved as it travels across the skin. Our results suggest, then, that the propagation of surface waves promotes the encoding of spectrally complex vibrations as the entire neural population is exposed to essentially the same stimulus. We also discuss the implications of our results for biomechanical models of the skin.
A Practical Experience on the Impact of Plugins in Web Security

In an attempt to support customization, many web applications allow the integration of third-party server-side plugins that offer diverse functionality, but also open an additional door for security vulnerabilities. In this paper we study the use of static code analysis tools to detect vulnerabilities in the plugins of the web application. The goal is twofold: 1) to study the effectiveness of static analysis on the detection of web application plugin vulnerabilities, and 2) to understand the potential impact of those plugins in the security of the core web application. We use two static code analyzers to evaluate a large number of plugins for a widely used Content Manage-ment System. Results show that many plugins that are current-ly deployed worldwide have dangerous Cross Site Scripting and SQL Injection vulnerabilities that can be easily exploited, and that even widely used static analysis tools may present disappointing vulnerability coverage and false positive rates.
Increased Proportion of Variance Explained and Prediction Accuracy of Survival of Breast Cancer Patients with Use of Whole-Genome Multiomic Profiles

Whole-genome multiomic profiles hold valuable information for the analysis and prediction of disease risk and progression. However, integrating high-dimensional multilayer omic data into risk-assessment models is statistically and computationally challenging. We describe a statistical framework, the Bayesian generalized additive model ((BGAM), and present software for integrating multilayer high-dimensional inputs into risk-assessment models. We used BGAM and data from The Cancer Genome Atlas for the analysis and prediction of survival after diagnosis of breast cancer. We developed a sequence of studies to (1) compare predictions based on single omics with those based on clinical covariates commonly used for the assessment of breast cancer patients (COV), (2) evaluate the benefits of combining COV and omics, (3) compare models based on (a) COV and gene expression profiles from oncogenes with (b) COV and whole-genome gene expression (WGGE) profiles, and (4) evaluate the impacts of combining multiple omics and their interactions. We report that (1) WGGE profiles and whole-genome methylation (METH) profiles offer more predictive power than any of the COV commonly used in clinical practice (e.g., subtype and stage), (2) adding WGGE or METH profiles to COV increases prediction accuracy, (3) the predictive power of WGGE profiles is considerably higher than that based on expression from large-effect oncogenes, and (4) the gain in prediction accuracy when combining multiple omics is consistent. Our results show the feasibility of omic integration and highlight the importance of WGGE and METH profiles in breast cancer, achieving gains of up to 7 points area under the curve (AUC) over the COV in some cases.
Some hypothesis tests for the covariance matrix when the dimension is large compared to the sample size

This paper analyzes whether standard covariance matrix tests work when dimensionality is large, and in particular larger than sample size. In the latter case, the singularity of the sample covariance matrix makes likelihood ratio tests degenerate, but other tests based on quadratic forms of sample covariance matrix eigenvalues remain well-defined. We study the consistency property and limiting distribution of these tests as dimensionality and sample size go to infinity together, with their ratio converging to a finite non-zero limit. We find that the existing test for sphericity is robust against high dimensionality, but not the test for equality of the covariance matrix to a given matrix. For the latter test, we develop a new correction to the existing test statistic that makes it robust against high dimensionality.
Social Perception of Bodybuilders

Engaging in bodybuilding, especially by a woman, may have a pervasive influence on the impressions others have of the bodybuilder. The first experiment examined the effects of the label bodybuilder on subjects' ratings of the probability that the stimulus person possessed gender-related characteristics. The second experiment was designed to determine whether female bodybuilders, compared to attractive and unattractive female nonbodybuilders, are (a) assumed to possess less socially desirable personality traits, (b) expected to lead less successful lives, and (c) viewed as less physically attractive. Results indicate that bodybuilding information plays a dominant role in influencing judgments. Stimulus persons who engage in bodybuilding are judged to be more likely to perform masculine role behaviors and less likely to be employed in feminine occupations, irrespective of gender. Female bodybuilders are viewed as relatively unattractive and are attributed with less desirable personality traits than are attr.
Transcription Activator-Like Effector Nucleases (TALEN)-Mediated Targeted DNA Insertion in Potato Plants

Targeted DNA integration into known locations in the genome has potential advantages over the random insertional events typically achieved using conventional means of genetic modification. Specifically integrated transgenes are guaranteed to co-segregate, and expression level is more predictable, which makes downstream characterization and line selection more manageable. Because the site of DNA integration is known, the steps to deregulation of transgenic crops may be simplified. Here we describe a method that combines transcription activator-like effector nuclease (TALEN)-mediated induction of double strand breaks (DSBs) and non-autonomous marker selection to insert a transgene into a pre-selected, transcriptionally active region in the potato genome. In our experiment, TALEN was designed to create a DSB in the genome sequence following an endogenous constitutive promoter. A cytokinin vector was utilized for TALENs expression and prevention of stable integration of the nucleases. The donor vector contained a gene of interest cassette and a promoter-less plant-derived herbicide resistant gene positioned near the T-DNA left border which was used to select desired transgenic events. Our results indicated that TALEN induced T-DNA integration occurred with high frequency and resulting events have consistent expression of the gene of interest. Interestingly, it was found that, in most lines integration took place through one sided homology directed repair despite the minimal homologous sequence at the right border. An efficient transient assay for TALEN activity verification is also described.
The Largest Group of Superficial Neocortical GABAergic Interneurons Expresses Ionotropic Serotonin Receptors

A highly diverse population of neocortical GABAergic inhibitory interneurons has been implicated in multiple functions in information processing within cortical circuits. The diversity of cortical interneurons is determined during development and primarily depends on their embryonic origins either from the medial (MGE) or the caudal (CGE) ganglionic eminences. Although MGE-derived parvalbumin (PV)- or somatostatin (SST)-expressing interneurons are well characterized, less is known about the other types of cortical GABAergic interneurons, especially those of CGE lineage, because of the lack of specific neuronal markers for these interneuron subtypes. Using a bacterial artificial chromosome transgenic mouse line, we show that, in the somatosensory cortex of the mouse, the serotonin 5-hydroxytryptamine 3A (5-HT3A) receptor, the only ionotropic serotonergic receptor, is expressed in most, if not all, neocortical GABAergic interneurons that do not express PV or SST. Genetic fate mapping and neurochemical profile demonstrate that 5-HT3AR-expressing neurons include the entire spectrum of CGE-derived interneurons. We report that, in addition to serotonergic responsiveness via 5-HT3ARs, acetylcholine also depolarizes 5-HT3AR-expressing neurons via nicotinic receptors. 5-HT3AR-expressing neurons in thalamocortical (TC) recipient areas receive weak but direct monosynaptic inputs from the thalamus. TC input depolarizes a subset of TC-recipient 5-HT3AR neurons as strongly as fast-spiking cells, in part because of their high input resistance. Hence, fast modulation of serotonergic and cholinergic transmission may influence cortical activity through an enhancement of GABAergic synaptic transmission from 5-HT3AR-expressing neurons during sensory process depending on different behavioral states.
Trade‐offs in the evolution of bumblebee colony and body size: a comparative analysis

Abstract Trade‐offs between life‐history traits – such as fecundity and survival – have been demonstrated in several studies. In eusocial insects, the number of organisms and their body sizes can affect the fitness of the colony. Large‐than‐average body sizes as well as more individuals can improve a colony's thermoregulation, foraging efficiency, and fecundity. However, in bumblebees, large colonies and large body sizes depend largely on high temperatures and a large amount of food resources. Bumblebee taxa can be found in temperate and tropical regions of the world and differ markedly in their colony sizes and body sizes. Variation in colony size and body size may be explained by the costs and benefits associated with the evolutionary history of each species in a particular environment. In this study, we explored the effect of temperature and precipitation (the latter was used as an indirect indicator of food availability) on the colony and body size of twenty‐one bumblebee taxa. A comparative analysis controlling for phylogenetic effects as well as for the body size of queens, workers, and males in bumblebee taxa from temperate and tropical regions indicated that both temperature and precipitation affect colony and body size. We found a negative association between colony size and the rainiest trimester, and a positive association between the colony size and the warmest month of the year. In addition, male bumblebees tend to evolve larger body sizes in places where the rain occurs mostly in the summer and the overall temperature is warmer. Moreover, we found a negative relationship between colony size and body sizes of queens, workers, and males, suggesting potential trade‐offs in the evolution of bumblebee colony and body size.
Got perspective? A theoretical view of fiscal impact analysis

In what has been described as a magisterial account of planning, John Friedmann (1987: 36) took the task of planning theory to solve ‘the meta-theoretical problem of how to make technical knowledge in planning effective in informing public actions’. Failure to do so, he argued, would mean that ‘planners will end up talking only to themselves and eventually will become irrelevant’. In this essay we want to argue that despite significant advances in planning theory since Friedmann threw down the gauntlet, a fundamental tension exists between technical knowledge and its role in public action and that this tension endures because of a lack of clarity of the relationship between the two. Allow us to explain. Planning knowledge is different from most other technical knowledge in that it cannot be first generated and then applied. As Donald Schon (1983) was teaching us, about the same time that Friedmann posed his challenge, rather than first reflect and then act, the epistemology of planning must cultivate the idea of reflection in action. In our view the lack of clarity is about the difference between the two positions: a) planning as connection between knowledge and action and b) planning as reflection in action (Verma, 1998a). The former accents the kind of public participation, outreach, consensus building, communication, and other approaches that have dominated the planning landscape. The latter demands, however, epistemological redress. It challenges us to bring concerns of the public at the level of knowledge generation. What does this mean when faced with fairly technical issues of models and methods? After all it is not prudent to expect the public to participate at that level and if broad outreach happens it is likely to be either by experts with technical knowledge or might include bystanders who would falsely legitimate the effort without contributing useful input. In our view, the solution to the problem lies at the level of planning research and pedagogy and we will argue that it warrants an Article
Global Genome Nucleotide Excision Repair is Organised into Domains Promoting Efficient DNA Repair in Chromatin

The rates at which lesions are removed by DNA repair can vary widely throughout the genome with important implications for genomic stability. To study this, we measured the distribution of nucleotide excision repair (NER) rates for UV-induced lesions throughout the budding yeast genome. By plotting these repair rates in relation to genes and their associated flanking sequences, we reveal that in normal cells, genomic repair rates display a distinctive pattern, suggesting that DNA repair is highly organised within the genome. Furthermore, by comparing genome-wide DNA repair rates in wild-type cells, and cells defective in the global genome-NER (GG-NER) sub-pathway, we establish how this alters the distribution of NER rates throughout the genome. We also examined the genomic locations of GG-NER factor binding to chromatin before and after UV irradiation revealing that GG-NER is organised and initiated from specific genomic locations. At these sites, chromatin occupancy of the histone acetyl transferase Gcn5 is controlled by the GG-NER complex, which regulates histone H3 acetylation and chromatin structure, thereby promoting efficient DNA repair of UV-induced lesions. Chromatin remodeling during the GG-NER process is therefore organized into these genomic domains. Importantly, loss of Gcn5, significantly alters the genomic distribution of NER rates, a finding that has important implications for the effects of chromatin modifiers on the distribution of mutations that arise throughout the genome.
Activation and Proteolytic Activity of the Treponema pallidum Metalloprotease, Pallilysin

Treponema pallidum is a highly invasive pathogen that undergoes rapid dissemination to establish widespread infection. Previous investigations identified the T. pallidum adhesin, pallilysin, as an HEXXH-containing metalloprotease that undergoes autocatalytic cleavage and degrades laminin and fibrinogen. In the current study we characterized pallilysin's active site, activation requirements, cellular location, and fibrin clot degradation capacity through both in vitro assays and heterologous treponemal expression and degradation studies. Site-directed mutagenesis showed the pallilysin HEXXH motif comprises at least part of the active site, as introduction of three independent mutations (AEXXH [H198A], HAXXH [E199A], and HEXXA [H202A]) abolished pallilysin-mediated fibrinogenolysis but did not adversely affect host component binding. Attainment of full pallilysin proteolytic activity was dependent upon autocatalytic cleavage of an N-terminal pro-domain, a process which could not occur in the HEXXH mutants. Pallilysin was shown to possess a thrombin cleavage site within its N-terminal pro-domain, and in vitro studies confirmed cleavage of pallilysin with thrombin generates a truncated pallilysin fragment that has enhanced proteolytic activity, suggesting pallilysin can also exploit the host coagulation process to facilitate protease activation. Opsonophagocytosis assays performed with viable T. pallidum demonstrated pallilysin is a target of opsonic antibodies, consistent with a host component-interacting, surface-exposed cellular location. Wild-type pallilysin, but not the HEXXA mutant, degraded fibrin clots, and similarly heterologous expression of pallilysin in the non-invasive spirochete Treponema phagedenis facilitated fibrin clot degradation. Collectively these results identify pallilysin as a surface-exposed metalloprotease within T. pallidum that possesses an HEXXH active site motif and requires autocatalytic or host-mediated cleavage of a pro-domain to attain full host component-directed proteolytic activity. Furthermore, our finding that expression of pallilysin confers upon T. phagedenis the capacity to degrade fibrin clots suggests this capability may contribute to the dissemination potential of T. pallidum.