Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteomic Investigation of the Response of Enterococcus faecalis V583 when Cultivated in Urine

Enterococcus faecalis is a robust bacterium, which is able to survive in and adapt to hostile environments such as the urinary tract and bladder. In this label-free quantitative proteomic study based on MaxQuant LFQ algorithms, we identified 127 proteins present in the secretome of the clinical vancomycin-resistant isolate E. faecalis V583 and we compared proteins secreted in the initial phase of cultivation in urine with the secretome during cultivation in standard laboratory medium, 2xYT. Of the 54 identified proteins predicted to be secreted, six were exclusively found after cultivation in urine including the virulence factor EfaA (“endocarditis specific antigen”) and its homologue EF0577 (“adhesion lipoprotein”). These two proteins are both involved in manganese transport, known to be an important determinant of colonization and infection, and may additionally function as adhesins. Other detected urine-specific proteins are involved in peptide transport (EF0063 and EF3106) and protease inhibition (EF3054). In addition, we found an uncharacterized protein (EF0764), which had not previously been linked to the adaptation of V583 to a urine environment, and which is unique to E. faecalis. Proteins found in both environments included a histone-like protein, EF1550, that was up-regulated during cultivation in urine and that has a homologue in streptococci (HlpA) known to be involved in bacterial adhesion to host cells. Up-regulated secreted proteins included autolysins. These results from secretome analyses are largely compatible with previously published data from transcriptomics studies. All in all, the present data indicate that transport, in particular metal transport, adhesion, cell wall remodelling and the unknown function carried out by the unique EF0764 are important for enterococcal adaptation to the urine environment. These results provide a basis for a more targeted exploration of novel proteins involved in the adaptability and pathogenicity of E. faecalis.
Systems with inheritance: dynamics of distributions with conservation of support, natural selection and finite-dimensional asymptotics

If we find a representation of an infinite-dimensional dynamical system as a nonlinear kinetic system with {\it conservation of supports} of distributions, then (after some additional technical steps) we can state that the asymptotics is finite-dimensional. This conservation of support has a {\it quasi-biological interpretation, inheritance} (if a gene was not presented initially in a isolated population without mutations, then it cannot appear at later time). These quasi-biological models can describe various physical, chemical, and, of course, biological systems. The finite-dimensional asymptotic demonstrates effects of {\it ``natural" selection}. The estimations of asymptotic dimension are presented. The support of an individual limit distribution is almost always small. But the union of such supports can be the whole space even for one solution. Possible are such situations: a solution is a finite set of narrow peaks getting in time more and more narrow, moving slower and slower. It is possible that these peaks do not tend to fixed positions, rather they continue moving, and the path covered tends to infinity at $t \rightarrow \infty$. The {\it drift equations} for peaks motion are obtained. Various types of stability are studied. In example, models of cell division self-synchronization are studied. The appropriate construction of notion of typicalness in infinite-dimensional spaces is discussed, and the ``completely thin" sets are introduced.
UGA hopping: a sport for nephrologists too?

The genetic information encoded by DNA is ultimately ex-pressed into specific polypeptides by way of transcriptionand translation. Transcription is the process whereby thecoding gene sequence is transferred into a messengerRNA (mRNA). Through translation, polypeptides aresynthesized at the ribosomes, collinearly with the sequenceof codons in mRNA. Codons are sets of three ribonucleo-tides in mRNA that signal the initiation, elongation and ter-mination stages of translation. With the exception of thenonsense codons (UAG, UAA and UGA), all codons havecorrespondingcomplementaryanti-codonsintransferRNA(tRNA) molecules. Each tRNA carries a specific aminoacid, which is incorporated into the elongating polypeptideaccording to the codon sequence in mRNA. The correctmRNA reading frame is defined at the start of translationbythestartcodon(AUG),whichcodesfor methionine.Ter-mination of translation is normally signalled by the occur-rence of any of the three codons for which no tRNA isavailable, hence named stop codons. Protein release factorsspecificallybindtostopcodons,mediatingthereleaseofthenewly synthesized polypeptide from the ribosome. How-ever, the stop codons are not equally effective in determin-ing the efficiency of translation termination, with therelative rank order of efficiency being UAA>UAG>UGA[1]. Whentranslationalreadingthroughstopcodonsoccurs,UAAandUAGusuallydirecttheadditionofglutamineintothenascentpolypeptide,whereastryptophanisincorporatedin response to UGA in bacteria [2]. Nonsense mutations are single-nucleotide alterations inthe DNA that directly change sense to nonsense codons,causing a premature stop of the mRNA translation process.Stop codons may also be generated by mutations that alterthe reading frame of mRNA, either as a result of insertionand/or deletion of a number of nucleotides not evenlydivisiblebythree,orofanabnormallysplicedRNA.Prema-tureterminationcodons(PTC)leadtotheformationoftrun-cated proteins that do not function properly. The frequencyof PTCs is rather variable, ranging from 5% to 70% ofreported mutations for different diseases [3–5]. Cellulardefence mechanisms against the potential deleteriousconsequences of PTCs involve the degradation of thetruncated proteins, and the detection and degradationof mRNAs containing these codons through nonsense-mediated mRNA decay (NMD) (Figure 1). NMD is aribosomal function that scans newly synthesizedmRNAs for the presence of PTCs in a pioneer roundof translation [6,7]. Normal stop codons are surrounded by upstream anddownstream sequences, which enhance the efficiency oftranslation termination [8,9]. As PTCs lack these surround-ing complementary signals, pharmacological approachesmay be devised that allow translational read-through ofin-frame PTCs, whilekeepingthe physiological stop codonactive, thus potentially yielding a full-length normal orfunctional protein (Figure 1) [10].
A Scalable Multi Keyword Search and RelevanceOriented Ranking for Searchable NetworkEncrypted data in Cloud Storage Systems

Secured Cloud Storage service allows the users to store and access their data remotely from various locations by using various secured data access protocols. With the advent of cloud storage services data owners started to outsource their complex data management systems from local sites to the commercial public cloud for great flexibility and economic savings. Due to the high security and reliability of cloud storage services most of the data owners are persisting their personal and sensitive information like emails, financial details, photo albums and some other important documents in cloud. To prevent the data stored in the cloud from unauthorized access and manipulations, data is encrypted before persist in cloud. Now a days the data owners have the interest to share their private outsourced data with a large number of authorized users, who might want to only retrieve certain specific data files by using the most popular keyword search on cloud data.Keyword search on encrypted huge data would become more time consuming task and less results relevance. In this paper we are introducing an scalablemulti-keyword search against the searchable encrypted data to allow multiple keywords in the search query and return the documents in order of their relevance to these keywords.A scalable Relevance Oriented Ranking-ROR is used to display the retrieved results in an efficient order for a given keyword search query. Experiments on sample data set in cloud shows that our approach is retrieving and displaying the data from cloud effectively for a given query.
Transperineal excision: A novel and alternative surgical approach for pelvic recurrence of rectal cancer.

Dis 2000;31:1093–5. 2. Mc Bride MO, Fisher M, Skinner CJ, et al. An unusual gastrointestinal presentation of leishmaniasis. Scand J Infect Dis 1995;27:297–8. 3. M L Alvarez-Nebreda, E Alvarez-Fernandez, S Rada, F Branas, E Maranon, M T Vidan, J A Serra-Rexach. Unusual duodenal presentation of leishmaniasis. J Clin Pathol 2005;58:1321–2. 4. Berman JD. Human leishmaniasis: clinical, diagnostic and chemotherapeutic developments in the last 10 years. Clin Infect Dis 1997;24:684–703.
Emotion in dialogic interaction : advances in the complex

1. Foreword 2. Part I. Addressing the complex 3. Emotions: The simple and the complex (by Weigand, Edda) 4. Universality vs. culture-specificity of emotion (by Danes, Frantisek) 5. Emotions in language and communication (by Cmejrkova, Svetla) 6. Emotions, language, and context (by Bazzanella, Carla) 7. Body, passions and race in classical theories of language and emotion (by Joseph, John E.) 8. Part II. Communicative means for expressing emotions 9. Interjections in a contrastive perspective (by Aijmer, Karin) 10. When did we start feeling guilty? (by Teubert, Wolfgang) 11. Joy, astonishment and fear in English, German and Russian: A corpus-based contrastive-semantic analysis (by Dem'jankov, Valerij) 12. Ambivalence as a dialogic frame of emotions in conflict (by Stamenov, Maxim I.) 13. Part III. Emotional principles in dialogue 14. The Role of Emotions in Normative Discourse and Persuasion (by Walrod, Michael R.) 15. Anticipation of public emotions in TV debates (by Bollow, Jorn) 16. Interpreting emotions in literary dialogue (by Weizman, Elda) 17. The author-reader-text emotional bond in the literary action game (by Sovran, Tamar) 18. On the inseparability of emotion and reason in argumentation (by Plantin, Christian) 19. General index 20. List of contributors
Reconciling Mining with the Conservation of Cave Biodiversity: A Quantitative Baseline to Help Establish Conservation Priorities

Caves pose significant challenges for mining projects, since they harbor many endemic and threatened species, and must therefore be protected. Recent discussions between academia, environmental protection agencies, and industry partners, have highlighted problems with the current Brazilian legislation for the protection of caves. While the licensing process is long, complex and cumbersome, the criteria used to assign caves into conservation relevance categories are often subjective, with relevance being mainly determined by the presence of obligate cave dwellers (troglobites) and their presumed rarity. However, the rarity of these troglobitic species is questionable, as most remain unidentified to the species level and their habitats and distribution ranges are poorly known. Using data from 844 iron caves retrieved from different speleology reports for the Carajás region (South-Eastern Amazon, Brazil), one of the world's largest deposits of high-grade iron ore, we assess the influence of different cave characteristics on four biodiversity proxies (species richness, presence of troglobites, presence of rare troglobites, and presence of resident bat populations). We then examine how the current relevance classification scheme ranks caves with different biodiversity indicators. Large caves were found to be important reservoirs of biodiversity, so they should be prioritized in conservation programs. Our results also reveal spatial autocorrelation in all the biodiversity proxies assessed, indicating that iron caves should be treated as components of a cave network immersed in the karst landscape. Finally, we show that by prioritizing the conservation of rare troglobites, the current relevance classification scheme is undermining overall cave biodiversity and leaving ecologically important caves unprotected. We argue that conservation efforts should target subterranean habitats as a whole and propose an alternative relevance ranking scheme, which could help simplify the assessment process and channel more resources to the effective protection of overall cave biodiversity.
Performance appraisal : state of the art in practice

Foreword - Manual London. Preface. The Authors. THE PERFORMANCE APPRAISAL ENVIRONMENT. 1. Effective Performance Management: A Focus on Precison, Customers, and Situational Constraints. 2. Current Legal Issues in Performance Appraisal. 3. International Performance Measuement and Management. 4. Performance Appraisal in a Quality Context: A New Look at an Old Problem. 5. Games Raters Play: Politics, Strategies and Impression Management in Performance Appraisal. METHODS OF APRAISING PERFORMANCE. 6. Creating Performance Management Systems That Promote Perceptions of Fairness. 7. Performance Appraisal in Team Settings. 8. Using Multisource Feedback for Employee Development and Personnel Decisions. 9. The Advantage and Pitfalls of Self-Assessment in Organizations. 10. Evaluating Executive Performance. 11. Training Raters to Increase the Accuracy of Appraisals and the Usefulness of Feedback. LINKING APPRAISALS TO THE LARGER HUMAN PERFORMANCE SYSTEM. 12. Linking Appraisals to Individual Development and Training. 13. Performance-Based Pay Plans. 14. Lessons Learrned: Research Implications for Performance Appraisal and Management Practices. Name Index. Subject Index.
Reflections on distributed leadership

Why the interest? Distributed leadership is a concept that is finding increasing support and is receiving widespread interest in the practitioner and research communities. So the question of ‘why the interest in distributed leadership? ’ is worth pursuing. While reasons for the contemporary interest certainly vary, it is suggested that reasons for the popularity of ‘distributed leadership’ are three-fold. First, the notion of distributed leadership has a descriptive power: it captures the forms of practice implicit in professional learning communities and communities of practice. It is difficult to envisage how communities of practice operate unless leadership and other organisational components are distributed. Wenger et al (2002) suggest that “distributed communities cross multiple types of boundaries and share ideas and insights”. In the increasingly complex world of education this has an immediate and powerful resonance. A second reason for the interest in distributed leadership resides in its representational power, in the fact that the organisational structure and basis of schooling is changing. In many countries there is a growing recognition that the old organisational structures of schooling simply do not fit the requirements of learning in the 21st century. Therefore, there are new models of schooling emerging, largely based on different collaborations and networking.While the terms for these new forms of schooling may vary from country to country (i.e. federations, partnerships, and networked learning communities) they essentially represent new and more complex organisational approaches to schooling. Implicit within these new forms is a requirement for leadership practices that are lateral rather than vertical, and for leadership that crosses organisational boundaries. Consequently, distributed leadership offers a way of thinking about leadership practice that accommodates new organisational forms and structures. A third reason for the interest in distributed leadership lies in its normative power; it reflects current leadership practice in schools.The growth of what Gronn (2003) has termed “greedy work” in schools has resulted in the expansion of leadership tasks and has required leadership to be actively shared within the school. The model of the singular leader is gradually being replaced with leadership that is premised upon teams rather than individuals, with greater emphasis being placed upon teachers as leaders (Harris, 2004). Consequently, the term ‘distributed leadership’ captures and reflects the evolving model of leadership in many schools encompassing multiple sources of influence and guidance.
The body doesn’t lie: a somatic approach to the study of emotions in world politics

The New York Times, December 27: A12. Smith, Adam. 2011 [1759]. The Theory of Moral Sentiments. London: Guttenberg. Sparks, Allister. 1994. Tomorrow is Another Country: The Inside Story of South Africa's Negotiated Revolution. Sandton, SA: Struik Books. Staub, Ervin. 2011. Overcoming Evil: Genocide, Violent Conflict, and Terrorism. Oxford: Oxford University Press. Sylvester, Christine. 2002. Feminist International Relations: An Unfinished Journey. Cambridge: Cambridge University Press. _____ 2011. “The Forum: Emotion and the Feminist IR Researcher. ” International Studies Review 13:687–708. Taylor, Shelly E. , Laura Cousino Klein, Brian P. Lewis, Tara L. Gruenewald, Regan A. R. Gurung, and John A. Updegraff 2002. “Biobehavioral Responses to Stress in Females: Tend and Befriend, not Fight or Flight. ” In Foundations in Social Neuroscience, edited by John T. Cacioppo, Gary G. Bernston, Shelley E. Taylor, and Daniel L. Schacter, 661–93. Cambridge, MA: MIT Press. Tutu, Desmond. 1999. No Future without Forgiveness. New York: Doubleday. Watson, Jeanne C. , and Leslie S. Greenberg. 2009. “Empathic Resonance: A Neuroscience Perspective. ” In The Social Neuroscience of Empathy, edited by Jean Decity and William Ickes, 125–37. Cambridge, MA: MIT Press. White, Ralph K. 1984. Fearful Warriors: A Psychological Profile of US-Soviet Relations. New York: Free Press. Zak, Paul J. 2011. “The Physiology of Moral Sentiments. ” Journal of Economic Behavior & Organization 77:53–65. Zaki, Jamil, and Kevin N. Ochsner. 2012. “The Neuroscience of Empathy: Progress, Pitfalls and Promise. ” Nature Neuroscience 15(5):675–80.
Efficient temporal keyword search over versioned text

Modern text analytics applications operate on large volumes of temporal text data such as Web archives, newspaper archives, blogs, wikis, and micro-blogs. In these settings, searching and mining needs to use constraints on the time dimension in addition to keyword constraints. A natural approach to address such queries is using an inverted index whose entries are enriched with valid-time intervals. It has been shown that these indexes have to be partitioned along time in order to achieve efficiency. However, when the temporal predicate corresponds to a long time range, requiring the processing of multiple partitions, naive query processing incurs high cost of reading of redundant entries across partitions. We present a framework for efficient approximate processing of keyword queries over a temporally partitioned inverted index which minimizes this overhead, thus speeding up query processing. By using a small synopsis for each partition we identify partitions that maximize the number of final non-redundant results, and schedule them for processing early on. Our approach aims to balance the estimated gains in the final result recall against the cost of index reading required. We present practical algorithms for the resulting optimization problem of index partition selection. Our experiments with three diverse, large-scale text archives reveal that our proposed approach can provide close to 80% result recall even when only about half the index is allowed to be read.
Cache behavior of combinator graph reduction

The results of cache-simulation experiments with an abstract machine for reducing combinator graphs are presented. The abstract machine, called TIGRE, exhibits reduction rates that, for similar kinds of combinator graphs on similar kinds of hardware, compare favorably with previously reported techniques. Furthermore, TIGRE maps easily and efficiently onto standard computer architectures, particularly those that allow a restricted form of self-modifying code. This provides some indication that the conventional "stored program" organization of computer systems is not necessarily an inappropriate one for functional programming language implementations. This is not to say, however, that present day computer systems are well equipped to reduce combinator graphs. In particular, the behavior of the cache memory has a significant effect on performance. In order to study and quantify this effect, trace-driven cache simulations of a TIGRE graph reducer running on a reduced instruction-set computer are conducted. The results of these simulations are presented with the following hardware-cache parameters varied: cache size, block size, associativity, memory update policy, and write-allocation policy. To begin with, the cache organization of a commercially available system is used and then the performance sensitivity with respect to variations of each parameter are measured. From the results of the simulation study, a conclusion is made that combinator-graph reduction using TIGRE runs most efficiently when using a cache memory with an allocate-on-write-miss strategy, moderately large block size (preferably with subblock placement), and copy-back memory updates.
Constituent similarity and systematicity: The limits of first-order connectionism

Standard feedforward and recurrent networks cannot support strong systematicity when constituents are presented as local input/output vectors. To explain systematicity connectionists must either: (1) develop alternative models, or (2) justify the assumption of similar (non-local) constituent representations prior to the learning task. I show that the second commonly presumed option cannot account for systematicity, in general. This option, termed first-order connectionism, relies upon established spatial relationships between common-class constituents to account for systematic generalization: inferences (functions) learnt over, for example, cats, extend systematically to dogs by virtue of both being nouns with similar internal representations so that the function learnt to make inferences employing one simultaneously has the capacity to make inferences employing the other. But, humans generalize beyond common-class constituents. Cross-category generalization (e.g. inferences that require treating mango as a colour, rather than a fruit) makes having had the necessary common context to learn similar constituent representations highly unlikely. At best, the constituent similarity proposal encodes for one binary relationship between any two constituents, at any one time. It cannot account for inferences, such as transverse patterning, that require identifying and applying one of many possible binary constituent relationships that is contingent on a third constituent (i.e. ternary relationship). Connectionists are, therefore, left with the first option which amounts to developing models with the symbol-like capacity to represent explicitly constituent relations independent of constituent contents, such as in tensor-related models. However, rather just simply implementing symbol systems, I suggest reconciling connectionist and classical frameworks to overcome their individual limitations.