Miracle-dz/UniFAR-FTUs huggingface dataset:
Interplay between tolerance mechanisms to copper and acid stress in Escherichia coli

Significance Copper (Cu) is an essential trace metal nutrient in health and is increasingly recognized for its role in the control of infection. The pathogen Escherichia coli encounters host niches with mild to high acidity and elevated copper levels. Our study shows that this bacterium can alter its metabolism and harness the amino acid glutamine to suppress the effects of acid stress and copper toxicity. Given the abundance of glutamine in systemic circulation and its importance in the host immune system, our work provides a new insight into the ways in which bacterial pathogens can adapt and survive host-imposed antibacterial strategies. Copper (Cu) is a key antibacterial component of the host innate immune system and almost all bacterial species possess systems that defend against the toxic effects of excess Cu. The Cu tolerance system in Gram-negative bacteria is composed minimally of a Cu sensor (CueR) and a Cu export pump (CopA). The cueR and copA genes are encoded on the chromosome typically as a divergent but contiguous operon. In Escherichia coli, cueR and copA are separated by two additional genes, ybaS and ybaT, which confer glutamine (Gln)-dependent acid tolerance and contribute to the glutamate (Glu)-dependent acid resistance system in this organism. Here we show that Cu strongly inhibits growth of a ∆copA mutant strain in acidic cultures. We further demonstrate that Cu stress impairs the pathway for Glu biosynthesis via glutamate synthase, leading to decreased intracellular levels of Glu. Addition of exogenous Glu rescues the ∆copA mutant from Cu stress in acidic conditions. Gln is also protective but this relies on the activities of YbaS and YbaT. Notably, expression of both enzymes is up-regulated during Cu stress. These results demonstrate a link between Cu stress, acid stress, and Glu/Gln metabolism, establish a role for YbaS and YbaT in Cu tolerance, and suggest that subtle changes in core metabolic pathways may contribute to overcoming host-imposed copper toxicity.
Matching Local Self-Similarities across Images and Videos

We present an approach for measuring similarity between visual entities (images or videos) based on matching internal self-similarities. What is correlated across images (or across video sequences) is the internal layout of local self-similarities (up to some distortions), even though the patterns generating those local self-similarities are quite different in each of the images/videos. These internal self-similarities are efficiently captured by a compact local "self-similarity descriptor"', measured densely throughout the image/video, at multiple scales, while accounting for local and global geometric distortions. This gives rise to matching capabilities of complex visual data, including detection of objects in real cluttered images using only rough hand-sketches, handling textured objects with no clear boundaries, and detecting complex actions in cluttered video data with no prior learning. We compare our measure to commonly used image-based and video-based similarity measures, and demonstrate its applicability to object detection, retrieval, and action detection.
Nanodiamond–Gutta Percha Composite Biomaterials for Root Canal Therapy

Root canal therapy (RCT) represents a standard of treatment that addresses infected pulp tissue in teeth and protects against future infection. RCT involves removing dental pulp comprising blood vessels and nerve tissue, decontaminating residually infected tissue through biomechanical instrumentation, and root canal obturation using a filler material to replace the space that was previously composed of dental pulp. Gutta percha (GP) is typically used as the filler material, as it is malleable, inert, and biocompatible. While filling the root canal space with GP is the standard of care for endodontic therapies, it has exhibited limitations including leakage, root canal reinfection, and poor mechanical properties. To address these challenges, clinicians have explored the use of alternative root filling materials other than GP. Among the classes of materials that are being explored as novel endodontic therapy platforms, nanodiamonds (NDs) may offer unique advantages due to their favorable properties, particularly for dental applications. These include versatile faceted surface chemistry, biocompatibility, and their role in improving mechanical properties, among others. This study developed a ND-embedded GP (NDGP) that was functionalized with amoxicillin, a broad-spectrum antibiotic commonly used for endodontic infection. Comprehensive materials characterization confirmed improved mechanical properties of NDGP over unmodified GP. In addition, digital radiography and microcomputed tomography imaging demonstrated that obturation of root canals with NDGP could be achieved using clinically relevant techniques. Furthermore, bacterial growth inhibition assays confirmed drug functionality of NDGP functionalized with amoxicillin. This study demonstrates a promising path toward NDGP implementation in future endodontic therapy for improved treatment outcomes.
Evolving Collective Behaviors With Diverse But Predictable Sensor States

Artificial evolution of collective behaviors can be implemented in different ways. Here, we extend the approach of Hamann (2014). The underlying concept is that the brain is permanently trying to predict future perceptions and a state of well-being is a state that allows for precise predictions (Friston, 2010). Striving for maximal prediction success needs to be complemented by a force that implements curiosity and exploration. In this abstract we present an extended method diverse-prediction that rewards not only for correct predictions but also for each visited sensory state. This proves to be a better approach compared to the method prediction (Hamann, 2014). As in the preliminary work (Hamann, 2014), we evolve pairs of artificial neural networks (ANN). One is predicting future sensor input and the other ANN outputs the next action. In our case study we simulate a homogeneous swarm (all agents share the same genome) of N = 20 agents (1st concept of population) that move in 1-d on a ring of circumference L. The agents have 4, discrete sensors covering 4 regions of the agent’s vicinity and output 1 for ‘there is at least 1 neighbor’ or 0 otherwise. The available actions are: move forward or invert the heading. We evolve pairs of ANN with a population of size 50 (2nd concept of population) for 75 generations in 200 independent runs for each tested setting. Fitness for prediction rewards good predictions of sensor values. Fitness for diverse-prediction rewards for visiting more sensor states (combinations of sensor values) and making good predictions in those states. For that, we sum up the ratios between the number of correct predictions for each visited sensor state and the number of visits of that state over the whole swarm over time. Generally a desired result is a well explored behavior space combined with precise predictions. We check the degree of exploration by investigating a 2d projection of behavior space. One dimension is covered distance which is the sum of the distances covered by the agents normalized by the considered time period and swarm size. Second dimension is the largest cluster size which is the maximum number of agents within sensor range normalized by swarm size. Fig. 1 (top) shows results for L = 50 but 3 settings were tested: high (L = 5), medium (L = 20), Figure 1: top: results of evolved behaviors for L=50; bottom: results from chi-squared test for L ∈ {5, 20, 50}.
Patch tests for diagnosis of delayed hypersensitivity to cephalosporins.

BACKGROUND Few studies have reported delayed hypersensitivity reactions to systemically administered cephalosporins. The diagnostic procedures and extracts for these reactions are not standardized, and little is known about the extent of cross reactivity among different cephalosporins. CASES REPORT We report 2 cases of delayed hypersensitivity reactions due to cephalosporins presenting as erythrodermia. Case 1. An 80-year-old man developed generalized pruritus and erythema 2-3 days after starting treatment with cefuroxime. The drug was stopped and antihistamines and corticosteroids were administered. The patient improved 5-6 days later, and mild superficial desquamation was observed. Case 2. A 66-year-old woman experienced similar symptoms 4-5 days after beginning cefazolin. She reported a similar reaction with ceftazidime 8 years previously. METHODS AND RESULTS Skin prick tests and specific IgE against penicillin G and V, amoxicillin, ampicillin and cephalosporins were negative. Intradermal tests with ceftazidime and cefazolin were positive in case 2 at delayed reading. Patch tests using benzylpenicillin, ampicillin, amoxicillin, several cephalosporins, aztreonam and imipenem were positive to all the cephalosporins tested (at 48 and 96 hours) and were negative to the other betalactams. Controlled administration of amoxicillin, benzylpenicillin, aztreonam and imipenem was well tolerated by both patients. CONCLUSIONS 1) We report 2 cases of delayed hypersensitivity reactions due to cephalosporins presenting as erythrodermia. 2) Epicutaneous tests were useful for diagnosis. 3) Both patients tested positive to all cephalosporins and negative to other betalactams.
Topology-Transparent Scheduling via the Chinese Remainder Theorem

This paper proposes a novel scheme for the design of topology-transparent scheduling (TTS) in mobile ad hoc networks (MANETs), based on the Chinese remainder theorem (CRT). TTS can provide each node with guaranteed success in each schedule without any detailed topology information and yields a guaranteed upper bound on the transmission delay of each packet at every node in a MANET. In general, TTS requires two global constraints on the number of nodes in the MANET and the maximum nodal degree of the graph representing connectivity of the MANET. Due to the inherent mobility of MANETs, the maximum nodal degree, however, cannot be available or easily estimated. To eliminate the requirement for the maximum nodal degree, this paper proposes TTS via the CRT. By the redundancy property of the Chinese remainder representation, the proposed CRT-based scheme not only preserves the advantages of providing guaranteed success in each schedule with only the global constraint on the number of nodes in the MANET, but also offers flexibility in constructing TTS. To have a better transmission delay bound for a node with lower interference, this paper also introduces two threaded counterparts of the proposed CRT-based scheme. This paper provides performance analyses for the proposed CRT-based scheme and its threaded counterparts. Numerical results demonstrate that TTS via the CRT can outperform existing schemes, especially in scenarios with harsh interference, and is a versatile approach for the design of TTS.
Surgical Treatment of Chronic Pancreatitis

Chronic pancreatitis (CP) is a benign inflammatory process of the pancreas. Progression of this disease results in structural changes with replacement of functional exocrine and endocrine parenchyma by a fibrotic and inflammatory tissue, often evident as an inflammatory mass. The consequences are diabetes mellitus, exocrine insufficiency, and severe recurrent upper abdominal pain, often resulting in a significant reduction in the quality of life. Additionally, the inflammatory process or the formation of pseudocysts can cause local complications such as obstruction of the pancreatic duct, bile duct or the duodenum. Due to lack of causal therapy, treatment aims at pain relief and substitution of exocrine and endocrine insufficiency. However, many patients require additional therapy for effective pain relief or treatment of local complications. Whereas a lot of these patients undergo repetitive endoscopic interventions, surgical drainage results in better long-term outcome. In patients with an inflammatory mass of the pancreatic head, surgical resection procedures provide good short and long-term results, especially in terms of pain relief. This article summarizes indications and potential of endoscopic/interventional and surgical therapy and gives an overview of surgical techniques with special focus on organ-sparing procedures such as the duodenum preserving pancreatic head resection and its variants. Whereas exocrine and endocrine insufficiency may progress, adequate surgical therapy can provide effective long-term pain relieve and improvement in the quality of life in patients with CP. Background, definition and epidemiology
Surface tensions, surgery, bodily boundaries and the social self

Surface Tensions is a book about the transformation of lives after the transformation of a body. It is an investigation of the effects that take place upon a person’s ‘subjectivity’ after undergoing certain types of surgery. Qualitative interviews with people who have had amputations, stoma, mastectomy and transplants of various kinds form the empirical bedrock of this study. Described by Lenore Manderson as ‘catastrophies of the body’, the author describes her work as focusing on manipulations on the surface of the body or reconstructions of its boundaries after undesired corporeal changes. The aim to examine individual transformations makes the book, in one sense, a study of the lives of those who acquired a particular type of impairment, locating attention primarily on the individual as considered in isolation rather than examining the wider ramifications of a disabling society. The text is structured by a variety of qualitative interviews conducted with individuals who are refiguring the contours of their post-surgery ‘self’. Manderson’s navigation of her interviewees’ responses to what she considers to be their ‘new bodies’ are compared with and related to the work of artists who have produced cultural products in reactions to their ‘new bodies’. The emphasis is upon celebrating those who re-draw boundaries of their bodies against the hegemonic values of a society that demands health of its members’ population. At the centre of Manderson’s argument is the way in which surgical interventions on the body create surface tensions that necessitate a renegotiation of the contours of both subjectivity and the body. Manderson’s work is driven forward by the question of how people make sense of the ‘new constraints and contingencies’ (23) in the rebuilding of the self after such surgeries. How people view themselves after undergoing ‘the urgent surgery to excise an aggressive cancer or to save a limb crushed by a fallen bar of steel’ (23), it is about life after rather than during a medical crisis. Deploying a metaphor from one her interviewees, Manderson wonders that if the body is a coat to the soul, then ‘is the soul, or the self, unscathed when the fabric is frayed and the seams restitched? ’ (23). The strategies that people have used to ‘re-stitch’ subjectivity after surgical intervention are, therefore, the real object of enquiry. ‘Catastrophes of the body’ are assumed to engender resulting catastrophes in subjectivity. Subjectivity, for Manderson, is here positioned as socially mediated. Manderson is careful to indicate many of the ways in which people have to renegotiate their sense of self in alliance with perceptions of others and the demands of society that valorises and privileges normalised image of the health body. The analysis is not dissimilar in my view to that of Erving Goffman in Stigma. The fragmentations of the image of oneself and the image of one’s body are identified in several of the interviewees’ accounts. The objectification of the site of surgery Disability & Society Vol. 27, No. 6, October 2012, 889–897
Privacy, Polygraphs and Work

The rights of prospective employees have been the subject of considerable dispute, both past and present. In recent years, this dispute has focused on the use of polygraphs to verify the claims which prospective employees make on employment application forms. With employee theft supposedly amounting to approximately ten billion dollars a year, with numerous businesses suffering sizeable losses and even being forced into bankruptcy by employee theft, significant and increasing numbers of employers have turned to the use of polygraphs.1 Their right to protect their property is in danger, they insist, and the use of the polygraph to detect and weed out the untrustworthy prospective employee is a painless, quick, economical, and legitimate way to defend this right. Critics, however, have questioned both the reliability and validity of polygraphs, as well as objected to the use of polygraphs as demeaning, affronts to human dignity, violations of selfincrimination prohibitions, expressions of employers' mistrust, and violations of privacy.2 Though there has been a great deal of discussion of the reliability and validity of polygraphs, there has been precious little discussion of the central moral issues at stake. Usually terms such as "dignity," "privacy," and "property rights" are simply bandied about with the hope that some favorable response will be evoked. The present paper seeks to redress this situation by discussing one important aspect of the above dispute? the supposed violation of personal privacy. Indeed, the violation of "a right to privacy" often appears to be the central moral objection to the use of polygraphs. However, the nature and basis of this claim have not yet been clearly established.3 If they could be, there would be a serious reason to oppose the use of polygraphs on prospective employees.
Behavioral foundations of reciprocity: experimental economics and evolutionary psychology

Laboratory experiments have generally supported the theorem that, in classical property rights environments, noncooperative behavior in markets yields efficient social outcomes. Experiments, however, regularly fail to support the game theoretic prediction of noncooperative behavior in small-group strategic interaction and in large-group public good environments. In these two types of experiments subjects frequently achieve more efficient social outcomes—they collect more money from the experimenter—than noncooperative game theory predicts. Many subjects in these experiments exhibit reciprocity even in single-play games. Evolutionary psychologists hypothesize that humans have evolved mental algorithms for identifying and punishing cheaters in social exchange. {JEL Al 1, A12, B41, C70, C72, C92)
What Do Planners Need to Know?

“Taking Our Bearings: Mapping a Relationship between Planning Practice, Theory, and Education” (Ozawa and Seltzer 1999) addresses an important issue: knowledge in planning. Several questions (e.g., Whose knowledge? What kinds of knowledge? ) that are raised in debates on the nature of planning are subsumed under this topic (e.g., Friedmann 1993; Alexander 1994). One of these is the question Connie P. Ozawa and Ethan P. Seltzer ask in their useful article: What do planners need to know? The answers to this question, of course, also depend—What kinds of planners? To do what? —but the article reveals its authors’ assumptions. In this way, we can infer that the knowledge this article is trying to identify is intended to make (Portland State University) planning graduates more effective practitioners. Although they do not identify their respondents by the domains of their practice, we can also infer that the kinds of planners Ozawa and Seltzer mean primarily practice physicaland land-use planning, development and perhaps some urban design, and zoning and development control. Their inquiry does not seem to extend to other fields of planning such as environmental planning, economic development or social planning, or transportation planning, which might have elicited somewhat different questions and answers. “Taking Our Bearings” is also quite unique in this discourse in its deployment of empirical data, its link between education and applications, and its synthesis of planning theory and practice. It contrasts with preceding empirical surveys (well referenced here), which are almost entirely atheoretical, and theoretical debates at such a high level of abstraction that it is sometimes difficult to fathom their practical implications (e.g., Hillier 1995; Crosta 1996; Alexander 1996). In this light, Ozawa and Seltzer’s effort to relate their findings to current debates in planning theory is welcome. Associating their survey’s competencies and skills (“modes of practice”) with competing theoretical planning models (“rational action” and “communicative discourse”), they conclude that the planning core curriculum, as the link between theory and practice, must move closer to the latter and incorporate more communicative practice. The transparency of its argument is one of the article’s merits. Skills and competencies are directly linked to specified forms of knowledge: analysis, communication, design, management, planning history and theory, and writing. But, as Einstein said, “It is theory that decides what we can observe. ” Ozawa and Seltzer’s theoretical construct, focusing on communicative practice, has biased their interpretation of their
ρ-uncertainty

The publication of transaction data, such as market basket data, medical records, and query logs, serves the public benefit. Mining such data allows for the derivation of association rules that connect certain items to others with measurable confidence. Still, this type of data analysis poses a privacy threat; an adversary having partial information on a person's behavior may confidently associate that person to an item deemed to be sensitive. Ideally, an anonymization of such data should lead to an inference-proof version that prevents the association of individuals to sensitive items, while otherwise allowing for truthful associations to be derived. Original approaches to this problem were based on value perturbation, damaging data integrity. Recently, value generalization has been proposed as an alternative; still, approaches based on it have assumed either that all items are equally sensitive, or that some are sensitive and can be known to an adversary only by association, while others are non-sensitive and can be known directly. Yet in reality there is a distinction between sensitive and non-sensitive items, but an adversary may possess information on any of them. Most critically, no antecedent method aims at a clear inference-proof privacy guarantee. In this paper, we propose ρ-uncertainty, the first, to our knowledge, privacy concept that inherently safeguards against sensitive associations without constraining the nature of an adversary's knowledge and without falsifying data. The problem of achieving ρ-uncertainty with low information loss is challenging because it is natural. A trivial solution is to suppress all sensitive items. We develop more sophisticated schemes. In a broad experimental study, we show that the problem is solved non-trivially by a technique that combines generalization and suppression, which also achieves favorable results compared to a baseline perturbation-based scheme.