Miracle-dz/UniFAR-FTUs huggingface dataset:
Vision Statement for Plant Physiology Genetically Encoded FRET Sensors for Visualizing Metabolites with Subcellular Resolution in Living Cells 1

What tools are there to determine the concentration of a particular molecular species in a physiological environment? Is it possible to visualize how its concentration varies across an organ, tissue, or cell? Is there a way to detect how metabolite levels change in response to environmental stimuli? Can these changes be monitored in real time? Can multiple analytes be measured simultaneously? Can these measurements be performed for a variety of structural and functional analyte classes? These are the central questions in the young field of metabolomics. No currently available technology addresses these issues in a satisfactory manner. Nonaqueous fractionation is static, invasive, has no cellular resolution, and is sensitive to artifacts. Spectroscopic methods such as nuclear magnetic resonance imaging and positron emission tomography provide dynamic data, but poor spatial resolution. The development of genetically encoded molecular sensors, which transduce an interaction of the target moleculewith a recognition element into amacroscopic observable, via allosteric regulation of one or more reporter elements, may provide answers to some of the questions. The recognition element may simply bind the target, bind and enzymatically convert the target, or may serve as a substrate for the target, as in the use of a specific target sequence in the construction of a protease sensor (Nagai and Miyawaki, 2004). The most common reporter element is a sterically separated donor-acceptor fluorescence resonance energy transfer (FRET) pair of spectral variants of the green fluorescent protein (GFP; Fehr et al., 2002), although single fluorescent proteins (Doi and Yanagawa, 1999) or enzymes (Guntas and Ostermeier, 2004) are viable as well. Some molecular sensors additionally employ a conformational actuator (most commonly a peptide which binds to one conformational state of the recognition element) to magnify the allosteric effect upon and resulting output of the reporter element (Miyawaki et al., 1997; Romoser et al., 1997; Kunkel et al., 2004).
DLVM: A MODERN COMPILER FRAMEWORK FOR NEURAL NETWORK DSLS

Many current approaches to deep learning make use of high-level toolkits such as TensorFlow, Torch, or Caffe. Toolkits such as Caffe have a layer-based programming framework with hard-coded gradients specified for each layer type, making research using novel layer types problematic. Toolkits such as Torch and TensorFlow define a computation graph in a host language such as Python, where each node represents a linear algebra operation parallelized as a compute kernel on GPU and stores the result of evaluation; some of these toolkits subsequently perform runtime interpretation over that graph, storing the results of forward calculations and reverse-accumulated gradients at each node. This approach is more flexible, but these toolkits take a very limited and ad-hoc approach to performing optimization. Also problematic are the facts that most toolkits lack type safety, and target only a single (usually GPU) architecture, limiting users’ abilities to make use of heterogeneous and emerging hardware architectures. We introduce a novel framework for high-level programming that addresses all of the above shortcomings.
Cause and effect of nondeterministic behavior in sequential and parallel SystemC simulators

Simulators are used to aid the design of computer systems. Together with the computational power of computer systems, the demands towards their simulators are growing regarding speed, flexibility, as well as the predictability of their behavior. To increase simulation speed, simulation models are abstracted and simulated in parallel. To reduce simulator development time and to provide the greatest possible modeling flexibility, SystemC allows models to be written using C++ without restrictions. All three means, especially when used in combination, also increase the difficulty to reason about the behavior of the resulting simulator, in the worst case leading to unpredictable simulation behavior. This may threaten the fitness of simulators for demanding use-cases like the debugging of race conditions. This work discusses likely causes and impact of nondeterministic simulator behavior. Three examples taken from real-life models are used to illustrate the matter.
In vitro susceptibilities of tropical strains of Aeromonas species from Queensland, Australia, to 22 antimicrobial agents

Greater than 90% of 131 strains of Aeromonas species were susceptible to the aminoglycosides, ureidopenicillins, extended-spectrum cephalosporins, aztreonam, quinolones, tetracycline, and chloramphenicol, and all were uniformly resistant to ampicillin. Except for amoxicillin-clavulanate, sulfonamide, trimethoprim, and trimethoprim-sulfamethoxazole, there was good correlation between the results obtained by the agar dilution and disk diffusion techniques.
Effects of amphotericin B on ion transport proteins in airway epithelial cells

Topical intranasal application of the antifungal Amphotericin B (AmphoB) has been shown as an effective medical treatment of chronic rhinosinusitis. Because this antibiotic forms channels in lipid membranes, we considered the possibility that it affects the properties and/or cell surface expression of ion channels/pumps, and consequently transepithelial ion transport. Human nasal epithelial cells were exposed apically to AmphoB (50 μM) for 4 h, 5 days (4 h daily), and 4 weeks (4 h daily, 5 days weekly) and allowed to recover for 18–48 h. AmphoB significantly reduced transepithelial potential difference, short‐circuit current, and the amiloride‐sensitive current. This was not due to generalized cellular toxicity as judged from normal transepithelial resistance and mitochondrial activity, but was related to inhibitory effects of AmphoB on ion transport proteins. Thus, cells exposed to AmphoB for 4 h showed decreased apical epithelial sodium channels (ENaC) activity with no change in basolateral Na+K+‐ATPase activity and K+ conductance, and reduced amount of αENaC, α1‐Na+K+‐ATPase, and NKCC1 proteins at the cell membrane, but no change in mRNA levels. After a 5‐day treatment, there was a significant decrease in Na+K+‐ATPase activity. After a 4‐week treatment, a decrease in basolateral K+ conductance and in αENaC and α1‐Na+K+‐ATPase mRNA levels was also observed. These findings may reflect a feedback mechanism aimed to limit cellular Na+ overload and K+ depletion subsequently to formation of AmphoB pores in the cell membrane. Thus, the decreased Na+ absorption induced by AmphoB resulted from reduced cell surface expression of the ENaC, Na+K+‐ATPase pump and NKCC1 and not from direct inhibition of their activities. © 2005 Wiley‐Liss, Inc.
Association and Interaction of the MAOA Promoter uVNTR Polymorphism with Suicide Attempts in Patients with Major Depressive Disorder

Background: This study aimed to explore the association between alleles of the MAOA uVNTR polymorphism and patients with major depressive disorder (MDD) who had attempted suicide, using multiple controls. The symptom profiles and personal characteristics in each group were also compared. Methods: Four different groups was included: 432 community controls, 385 patients with MDD who had not attempted suicide, 96 community subjects without mental disorders who had attempted suicide from emergency room in a general hospital, and 109 patients with MDD who had attempted suicide. Results: An intergroup difference in allelic frequency was found between female suicidal subjects from the community and female suicidal subjects with MDD (P = 0.028): heterozygosity for the long-form variant of the MAOA polymorphism (≧ 3.5 repeats) was found to be a potential protective factor against MDD among female suicidal subjects (OR = 0.396). By multivariate logistic regression analysis, the long-form variant was found to be associated with suicide after controlling for the effect of gender (P = 0.004). An interaction was also found between depression and suicide that showed a negative correlation with the MAOA long-form variant (P = 0.045, OR = 0.503). Structural equation modeling showed, neuroticism, extraversion, low levels of anxiety, high levels of depressive symptoms, and smoking were associated with suicidal behavior in MDD group, not in the group of subjects without MDD. Conclusion: The MAOA long-form variant was associated with enhanced vulnerability to suicide in the general population. Depressive symptoms and smoking were associated with suicide attempts, whereas anxiety was a protective factor against suicidal behavior in participants with MDD. Furthermore, we found that the MAOA longand short-form variants had different effects in controls and in patients with MDD, and the reverse effect of the long-form MAOA variant on MDD patients who had attempted suicide was revealed only by analysis of interactions. The results
Collaborative Linguistic Fieldwork: Practical Application of the Empowerment Model

Academic linguists working to document and describe minoritized and endangered languages share with speech community members a devotion to the language of study. For the academic, language provides a window into cognition and the capacity of the human mind. For the speech community member, language represents cultural heritage and, for many, a tie to place and a sense of identity. Both parties have a vested interest in the documentation, description, and preservation of lesser-spoken languages as a way to perpetuate global linguistic and cultural diversity and maintain ties to heritage. Many who conduct linguistic fieldwork with endangered languages have noted that the needs and desires of the speech community are often subordinated in favor of those of the academic linguist. Some academics fear that time spent meeting community needs diminishes the field-worker’s academic productivity. This paper describes several collaborative, community-based projects that address the needs of both academics and the speech community, using case-study examples from the author’s own fieldwork with a Kari’nja community in Suriname. In discussing each project, emphasis is given to practical methods of meeting needs of both the academic and speech communities, and to how this ensures more balanced participation of each in the linguistic fieldwork endeavor .
Recovery Support for Adolescents with Substance use Disorders: The Impact of Recovery Support Telephone Calls Provided by Pre-Professional Volunteers.

The present quasi-experiment examined the direct and indirect effects of recovery support telephone calls following adolescent substance use disorder treatment. Six-month outcome data from 202 adolescents who had received recovery support calls from primarily pre-professional (i.e., college-level social service students) volunteers was compared to 6-month outcome data from a matched comparison sample of adolescents (n = 404). Results suggested adolescents in the recovery support sample had significantly greater reductions in their recovery environment risk relative to the comparison sample (β = -.17). Path analysis also suggested that the reduction in recovery environment risk produced by recovery support calls had indirect impacts (via recovery environment risk) on reductions in social risk (β = .22), substance use (β = .23), and substance-related problems (β = .16). Finally, moderation analyses suggested the effects of recovery support calls did not differ by gender, but were significantly greater for adolescents with lower levels of treatment readiness. In addition to providing rare empirical support for the effectiveness of recovery support services, an important contribution of this study is that it provides evidence that recovery support services do not necessarily have to be "peer-based," at least in terms of the recovery support service provider having the experiential credentials of being "in recovery. " If replicated, this latter finding may have particularly important implications for helping increase the recovery support workforce.
Atheroma and diverticulosis.

Prolonged Anosmia I. MacIntyre, D.I. H. 709 Trauma to the Urinary Tract D. Lamont, F.R. C.S. ED . 710 Radiologists in Liverpool J. V. Occleshaw, M.D., F.F.R . 710 Treatment of Myasthenia S. Wolf, M.D. . 710 Aortic Aneurysm and Peptic Ulcer W. Wermut, M.D. . 710 Malaria and Sickle-cell Disease F. I. D. Konotey-Ahulu, M.R. C.P.; Anne Seymour, M.B . 710 Insulating Kidney Perfusion Fluid P. J. B. Smith, F.R. C.S. , and others . 711 Bleeding from Dialysis Shunt Sites J. R. Salaman, F.R. C.S. 711 Accidental Infection of Man with Mycoplasma caviae Auriol Hill . 711 Allergy to Iprindole (Prondole) with Hepatotoxicity A. D. Clift, M.B . 712 Congenital Dislocation of the Head of the Radius N. C. Roles, F.R. C.S . 712 Deaths from Tuberculosis B. H. R. Stack, M.R. C.P . 713 Paracetamol Overdose A. Lyell, F.R. C.P.GLASG. , and Suzanne L. Alexander, M.B. 713 Angina Pectoris S. H. Taylor, M.R. C.P.ED . 713 Community Physicians B. J. Essex, M.R. C.P., and others . 713 The Managerial Revolution J. R. Mathers, M.B. 714 N.H. S. Reorganization-Mark III U. P. Seidel, M.B. , D.P.M . 714 New Review Body H. E. Thomas, M.D . 714
Making Fast Consensus Generally Faster [ Technical Report ]

New multi-leader consensus protocols leverage the Generalized Consensus specification to enable low latency, even load balancing, and high parallelism. However these protocols introduce inherent costs with significant performance impact: they need quorums bigger than the minimum required to solve consensus, and need to track dependency relations among proposals. In this paper we present MPAXOS, an implementation of Generalized Consensus that provides fast decisions (i.e., delivery of a command in two communication delays) by leveraging quorums composed of a majority of nodes, and by exploiting workload locality. MPAXOS does not establish command dependencies based on conflicts, but it maps nodes to accessed objects, enforcing that commands accessing same objects are ordered by the same node. Our experimental evaluation confirms the effectiveness of MPAXOS, gaining up to 7× over state-ofthe-art Consensus and Generalized Consensus algorithms under partitioned data accesses, and up to 5.5× using the TPC-C workload.
Controlling information behaviour: the case for access control

ABSTRACT Intentional dissemination of information is a key role of information systems. Yet methods for controlling access to information – as opposed to data – are still in their infancy, especially in relation to the key ‘decision points' that need to be made regarding what information users can access when, and under what conditions. This paper presents the case for access control to be explicitly integrated into models of information behaviour, especially as they relate to information access on the relatively unregulated internet. An observational case study relating to information access in Indonesia – which is a highly regulated society – is presented, through advertising on rogue websites – in this case, behaviour which is strictly regulated in the physical world (such as the promotion of gambling) is relatively unchecked online; the absence of effective controls, as suggested by situational crime prevention theory [Clarke, R. V. G. , ed. 1997. Situational Crime Prevention. Criminal Justice Press] is reflected in the high levels of offending seen online. The extent to which information systems can manage information-seeking behaviour in a way that is consistent with regulatory or policy requirements in the online environment is discussed, with a view to establishing a foundation and terminology to modify information behaviour theory for the online environment.
Detecting global outliers from large distributed databases

In this paper, we present an innovative system, coined as DISTROD (a.k.a DISTRibuted Outlier Detector), for detecting outliers from distributed databases. DISTROD is able to effectively detect the so-called global outliers from distributed databases that are consistent with those produced by the centralized detection paradigm. Experimental evaluation demonstrates the good performance of DISTROD in terms of effectiveness and speed.
Comparing classical and embodied multimodal fusion for human-robot interaction

A robot that interacts with a human has to be able to interpret information from various input channels: it needs to understand and analyse the utterances by the human, it has to keep track of its own environment using sensors, and it needs to incorporate background knowledge about the task it was built for. Typically, a human-robot interaction system has various specialised system components that implement these abilities. Thus, the robot also needs to merge the information from its input channels so that it is able to complete its assigned task. This integration of information from input channels is called multimodal fusion. This thesis presents two approaches for multimodal fusion for a robot that jointly cooperates with a human partner. The first approach, which is called classical multimodal fusion, focusses on processing human utterances. For that, the robot processes speech and gestures of its human partner using methods from classical artificial intelligence to yield logical representations of the utterances. Following that, these representations are enhanced with further information from other input modalities of the robot. In contrast to that, in the second approach the robot generates representations for its own actions in relation to objects in its environment, so-called embodied multimodal fusion. Here, the system uses the data from its input channels to evaluate the relevance of its own actions for a given context. After a literature review, this thesis discusses the theoretical basis of both multimodal fusion approaches and presents how these methods can be implemented on a robot that is able to work together with a human on a common construction task, for which it processes multimodal input. These implementations were used in three human-robot interaction studies, in which näıve subjects worked together with the robot. The experiments were executed to study different aspects of joint action between human and robot. The results of the experiments reveal several interesting facts: the first experiment studies how the robot can explain building plans to the human. The results of the study show that the users preferred a plan explanation strategy in which the robot first names the target object and after that explains the single building steps. The first as well as the second experiment study the generation of referring expression in two different contexts. The results of the studies suggest that experiment participants rate the robot as a better dialogue partner when the robot makes full use of context information to generate referring expressions. Finally, the third experiment studies how humans perceive different roles of the robot in the interaction. The study shows that the users equally accept the robot as an instructor or as an equal partner and simply adjust their own behaviour to the robot’s role.
Elementary siphons of Petri nets and their application to deadlock prevention in flexible manufacturing systems

A variety of important Petri net-based methods to prevent deadlocks arising in flexible manufacturing systems (FMS) are to add some control places and related arcs to strict minimal siphons (SMS) such that no siphon can be emptied. Since the number of minimal siphons grows in general exponentially with respect to a Petri net size, their disadvantages lie in that they often add too many additional places to the net, thereby making the resulting net model much more complex than the original one. This paper explores ways to minimize the new additions of places while achieving the same control purpose. It proposes for the first time the concept of elementary siphons that are a special class of siphons. The set of elementary siphons in a Petri net is generally a proper subset of the set of all SMS. Its smaller cardinality becomes evident in large Petri net models. This paper proves that by adding a control place for each elementary siphon to make sure that it is marked, deadlock can be successfully prevented. Compared with the existing methods, the new method requires a much smaller number of control places and, therefore, is suitable for large-scale Petri nets. An FMS example is used to illustrate the proposed concepts and policy, and show the significant advantage over the previous methods.
Combined Topical Application of a Regenerative Agent With a Bandage Contact Lens for the Treatment of Persistent Epithelial Defects

Purpose: The aim of this study was to report 3 cases of persistent epithelial defects (PEDs) successfully treated with the combined topical application of a regenerative agent (RGTA; Cacicol20, OTR3, Paris, France) with a bandage contact lens (BCL). Methods: This is a case series. Results: Three patients suffering from a PED for 4–8 weeks and unresponsive to conventional therapy were treated with the combined application of an RGTA (Cacicol20) and a silicone hydrogel BCL. The PED healed in all patients after 4–21 days, and no side effects were noted. Conclusions: The combination of an RGTA (Cacicol20) with a BCL seems to be an effective treatment for PED.
Removal of U and Mo from water by immobilized Desulfovibrio desulfuricans in column reactors.

Intact cells of Desulfovibrio desulfuricans were immobilized in polyacrylamide gel and used to remove soluble U and Mo from water by enzymatically mediated reduction reactions in column reactors. Formate or lactate served as the electron donor and oxidized U(VI) and Mo(VI) species served as electron acceptors. Greater than 99% removal efficiencies were achieved for both metals with initial concentrations of 5 mg/L U and 10 mg/L Mo. Hydraulic residence times in the columns were between 24 and 36 h. Sulfate concentrations as high as 2000 mg/L did not inhibit reduction of U or Mo in the columns. However, nitrate inhibited uranium reduction at concentrations near 50 mg/L and inhibited molybdenum reduction at concentrations near 150 mg/L. The results indicate that enzymatic reduction of U and Mo by immobilized cells of D. desulfuricans may be a practical method for removing these contaminants from solution in continuous-flow reactors.