Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic and transcriptional analysis of absA, an antibiotic gene cluster‐linked two‐component system that regulates multiple antibiotics in Streptomyces coelicolor

In Streptomyces coelicolor, the AbsA1–AbsA2 two‐component system regulates the expression of multiple antibiotic gene clusters. Here, we show that the response regulator encoded by the absA2 gene is a negative regulator of these antibiotic gene clusters. A genetic analysis shows that the phosphorylated form of the AbsA2 response regulator (phospho‐AbsA2), generated by the cognate AbsA1 sensor histidine kinase, is required for normal growth phase regulation of antibiotic synthesis. In the absence of phospho‐AbsA2, antibiotics are produced earlier and more abundantly. Overexpression of AbsA1 also deregulates antibiotic synthesis, apparently shifting the AbsA1 protein from a kinase‐active to a phospho‐AbsA2 phosphatase‐active form. The absA1 and absA2 genes, which are adjacent, are located in one of the antibiotic gene clusters that they regulate, the cluster for the calcium‐dependent antibiotic (CDA). The absA genes themselves are growth phase regulated, with phospho‐AbsA2 responsible for growth phase‐related positive autoregulation. We discuss the possible role and mechanism of AbsA‐mediated regulation of antibiotic synthesis in the S. coelicolor life cycle.
Optimizing area coverage in Wireless Sensor Networks

Wireless Sensor Networks (WSNs) have inspired tremendous research interest in since the mid-1990s. Advancement in wireless communication and miniature electromechanical systems (MEMSs) have enabled the development of low-cost, low power, multi-functional, tiny sensor nodes that can sense the environment, perform data processing, and communicate with each other untethered over short distances. Most of the applications deployed over WSNs require strong coverage requirements, especially those related to the detection and tracking of distributed events. Moreover, these events are forwarded to the analysis center(s) through a set of sink nodes that locally gather data emanating from the elementary sensors. This paper proposes a coverage control scheme that adapts to the situation where multiple sink nodes are deployed within the monitored area. On the opposite to traditional coverage approaches that aim at guaranteeing a uniform density distribution, we place the sensor nodes in a manner that increases the coverage degree according to their proximity to a sink node. To reduce the complexity of the optimization process, we consider a discrete search space by structuring the monitored into a uniform grid. An evolutionary algorithm is then used to choose whether to activate or not sensor nodes within every cell of the grid. We conducted a set of simulations in order to evaluate the performance of the proposed strategy, mainly in ensuring multi-target tracking.
A Message Passing Algorithm for the Minimum Cost Multicut Problem

We propose a dual decomposition and linear program relaxation of the NP-hard minimum cost multicut problem. Unlike other polyhedral relaxations of the multicut polytope, it is amenable to efficient optimization by message passing. Like other polyhedral relaxations, it can be tightened efficiently by cutting planes. We define an algorithm that alternates between message passing and efficient separation of cycle-and odd-wheel inequalities. This algorithm is more efficient than state-of-the-art algorithms based on linear programming, including algorithms written in the framework of leading commercial software, as we show in experiments with large instances of the problem from applications in computer vision, biomedical image analysis and data mining.
Forward Genetic Analysis to Identify Determinants of Dopamine Signaling in Caenorhabditis elegans Using Swimming-Induced Paralysis

Disrupted dopamine (DA) signaling is believed to contribute to the core features of multiple neuropsychiatric and neurodegenerative disorders. Essential features of DA neurotransmission are conserved in the nematode Caenorhabditis elegans, providing us with an opportunity to implement forward genetic approaches that may reveal novel, in vivo regulators of DA signaling. Previously, we identified a robust phenotype, termed Swimming-induced paralysis (Swip), that emerges in animals deficient in the plasma membrane DA transporter. Here, we report the use and quantitative analysis of Swip in the identification of mutant genes that control DA signaling. Two lines captured in our screen (vt21 and vt22) bear novel dat-1 alleles that disrupt expression and surface trafficking of transporter proteins in vitro and in vivo. Two additional lines, vt25 and vt29, lack transporter mutations but exhibit genetic, biochemical, and behavioral phenotypes consistent with distinct perturbations of DA signaling. Our studies validate the utility of the Swip screen, demonstrate the functional relevance of DA transporter structural elements, and reveal novel genomic loci that encode regulators of DA signaling.
Multi group dynamic bandwidth allocation scheme in long reach PONs

With the progress in optical technology, the span of the Passive Optical Network (PONs) grows from 20km to 100km or even larger, known as super PONs or Long Reach PONs (LR-PONs). Because of the long span, an LR-PON can server many Optical Network Units (ONUs). In addition, since Optical Line Terminal (OLT) and ONUs are placed at a long distance from each others, the propagation delay of data and control signals between OLT and ONUs is long compared with traditional PONs. Since this long propagation delay increases packet delay and decreases channel utilization, it is an important challenge in an LR-PON. In this paper, we propose a new Dynamic Bandwidth Allocation (BDA) scheme called Multi Group DBA (MG-DBA) to improve utilization and to decrease packet delay. In MG-DBA, ONUs are classified into several groups. Therefore, when one group is sending its data to the OLT, the bandwidth for another group is simultaneously calculated. In addition, the OLT uses the Smallest Available Report First (SARF) for bandwidth calculation for each group to minimize packet delay. Simulation results show that the proposed MG-DBA algorithm can significantly reduce packet delay and improve channel utilization.
Differences and similarities between two frequently used assays for amyloid beta 42 in cerebrospinal fluid.

Amyloid β 42 (Aβ 42) concentrations in cerebrospinal fluid (CSF) are used to identify Alzheimer disease (AD) (1), but reported concentrations differ among studies, as does diagnostic accuracy (2). These differences may relate to the patient and control groups studied (3), processing and storage methods (4), intra- and interassay variation of the assays, or to the reagent antibodies used. A recent metaanalysis (2) stressed the importance of standardizing assays for Aβ–42 in CSF. In most studies, CSF Aβ 42 was reported to be decreased, but in 2 studies, CSF Aβ 42 was not significantly changed in AD (2), and in 1 study(5) even increased in the early stages of disease. These dissimilarities might reflect the specificities of the antibodies incorporated in the assays. The first aim of our study was to compare Aβ 42 concentrations measured by 2 different assays in the same CSF samples. The first assay, widely used in Europe (6), uses 2 monoclonal antibodies (mAbs) and detects the full-length Aβ 42 peptide, Aβ (1–42) (7). The second assay [Aβ (N–42)], used mainly in the United States (8), detects both full-length Aβ 42 and Aβ peptides truncated at the NH2 terminus (9). The second aim of our study was to compare diagnostic accuracies of the assays for patients with AD compared with controls without dementia and patients with frontotemporal lobar degeneration (FTLD). Finally, we investigated the relationship between CSF Aβ (1–42) and Aβ (N–42) concentrations and albumin ratio, age, disease duration, and disease severity. Between October 2000 and December 2002, we recruited 39 AD patients, 24 FTLD patients, and 30 non-dementia controls at the Alzheimer Center of the VU University Medical Center (VUMC). All patients underwent a standardized investigative battery (3). A diagnosis of “probable” AD was made according to the NINCDS-ADRDA criteria (10); the …
Evaluation of the In vitro and In vivo Antitumor Activity of Histone Deacetylase Inhibitors for the Therapy of Retinoblastoma

Purpose: To evaluate the potential utility of histone deacetylase inhibitors (HDACi) for treatment of retinoblastoma (RB). Experimental Design: Growth-inhibitory effects of HDACi [trichostatin A (TSA), suberoylanilide hydroxamic acid (SAHA), or MS-275] were assessed in human and transgenic murine RB cells. Effects of TSA and MS-275 were also assessed in combination with standard therapeutic agents for RB. Proapoptotic effects of MS-275 and TSA were evaluated by caspase-3/7 activity, Annexin V translocation, and/or Bim expression analyses. Effects of MS-275 on cell cycle distribution and reactive oxygen species levels were determined by flow cytometry. Retinal tissue morphology was evaluated in mice after local administration of MS-275. Analysis of retinal acetyl-histone levels was used to assess MS-275 delivery after systemic administration. Therapeutic effects of MS-275 were determined in transgenic mouse and rat ocular xenograft models of RB after i.p. injection of 20 mg/kg every other day for 21 or 13 days, respectively. Results: TSA, SAHA, and MS-275 dose dependently reduced RB cell survival. TSA and MS-275 showed additive growth-inhibitory effects in combination with carboplatin, etoposide, or vincristine. TSA and MS-275 increased caspase-3/7 activity. MS-275 increased Annexin V membrane translocation and induced G1 arrest. Cytotoxicity of MS-275 was dependent on increased reactive oxygen species levels and was reversed by antioxidant pretreatment. Intraocular administration of 1 μL of 10 μmol/L MS-275 did not alter ocular tissue morphology. Increased acetyl-histone levels confirmed MS-275 delivery to retinal tissue after systemic administration. MS-275 significantly reduced tumor burden in both mouse and rat models of RB. Conclusions: HDACi should be considered for clinical trials in children with RB.
Introduction to Green Security Games ( Extended Abstract )

Conservation agencies around the world are tasked with protecting endangered wildlife from poaching. Despite their substantial efforts, however, species are continuing to be poached to critical status and, in some cases, extinction. In South Africa, rhino poaching has seen a recent escalation in frequency; while only 122 rhinos were poached in 2009, a record 1215 rhinos were poached in 2014 (approximately 1 rhino every eight hours)[the Rhino International, 2015]. To combat poaching, conservation agencies send well-trained rangers to patrol designated protected areas. However, these agencies have limited resources and are unable to provide 100% coverage to the entire area at all times. Thus, it is important that agencies make the most efficient use of their patrolling resources, and we introduce Green Security Games (GSGs) as a tool to aid agencies in designing effective patrols. First introduced by [Von Stengel and Zamir, 2004] as a Leadership Game, Stackelberg Games have been applied in a variety of Security Game research (i.e., Stackelberg Security Games, or SSGs). In particular, the focus on randomization in Stackelberg Games lends itself to solving real-world security problems where defenders have limited resources, such as randomly allocating Federal Air Marshals to international flights [Tsai et al., 2009]. However, the SSG model focuses on generating an optimal defender strategy against a single defender-attacker interaction (e.g., a single terrorist attack). For domains where attacks occur frequently, such as in wildlife conservation, another type of Security Game is needed that effectively models the repeated interactions between the defender and the attacker. While still following the Leader-Follower paradigm of SSGs, GSGs have been developed as a way of applying Game Theory to assist wildlife conservation efforts, whether its to prevent illegal fishing [Haskell et al., 2014], illegal logging [Johnson et al., 2012], or wildlife poaching [Yang et al., 2014]. GSGs are similar to SSGs except that, in GSGs, the game takes place over N rounds. In SSGs, once the attacker makes a decision, the game is over, but in GSGs, the attacker (e.g., the poacher) and defender have multiple rounds in which they can adapt to each other’s choices in previous rounds. This multi-round feature of GSGs introduces some key research challenges that are being studied: (1) how can we incorporate the attacker’s previous choices into our model of their behavior, in order to improve the defender’s strategy, [Yang et al., 2014; Kar et al., 2015] and (2) how do we choose a strategy such that the long-term payoff (i.e., cumulative expected utility) is maximized [Fang et al., 2015]? In addition to exploring these open research questions, we also discuss field tests of the Protection Assistant for Wildlife Security (PAWS) software in Uganda and Malaysia.
Why Do Banks Hold Capital in Excess of Regulatory Requirements? A Functional Approach

This paper provides an explanation for the observation that banks hold on average a capital ratio in excess of regulatory requirements. We use a functional approach to banking based on Diamond and Rajan (2001) to demonstrate that banks can use capital ratios as a strategic tool for renegotiating loans with borrowers. As capital ratios affect the ability of banks to collect loans in a nonmonotonic way, a bank may be forced to exceed capital requirements. Moreover, high capital ratios may also constrain the amount a banker can borrow from investors. Consequently, the size of the banking sector may shrink.
HvrBase++: a phylogenetic database for primate species

HvrBase++ is the improved and extended version of HvrBase. Extensions are made by adding more population-based sequence samples from all primates including humans. The current collection comprises 13 873 hypervariable region I (HVRI) sequences and 4940 hypervariable region II (HVRII) sequences. In addition, we included 1376 complete mitochondrial genomes, 205 sequences from X-chromosomal loci and 202 sequences from autosomal chromosomes 1, 8, 11 and 16. In order to reduce the introduction of erroneous data into HvrBase++, we have developed a procedure that monitors GenBank for new versions of the current data in HvrBase++ and automatically updates the collection if necessary. For the stored sequences, supplementary information such as geographic origin, population affiliation and language of the sequence donor can be retrieved. HvrBase++ is Oracle based and easily accessible by a web interface (). As a new key feature, HvrBase++ provides an interactive graphical tool to easily access data from dynamically created geographical maps.
The DEP domain-containing protein TOE-2 promotes apoptosis in the Q lineage of C. elegans through two distinct mechanisms

Neuroblast divisions in the nematode Caenorhabditis elegans often give rise to a larger neuron and a smaller cell that dies. We have previously identified genes that, when mutated, result in neuroblast divisions that generate daughter cells that are more equivalent in size. This effect correlates with the survival of daughter cells that would normally die. We now describe a role for the DEP domain-containing protein TOE-2 in promoting the apoptotic fate in the Q lineage. TOE-2 localized at the plasma membrane and accumulated in the cleavage furrow of the Q.a and Q.p neuroblasts, suggesting that TOE-2 might position the cleavage furrow asymmetrically to generate daughter cells of different sizes. This appears to be the case for Q.a divisions where loss of TOE-2 led to a more symmetric division and to survival of the smaller Q.a daughter. Localization of TOE-2 to the membrane is required for this asymmetry, but, surprisingly, the DEP domain is dispensable. By contrast, loss of TOE-2 led to loss of the apoptotic fate in the smaller Q.p daughter but did not affect the size asymmetry of the Q.p daughters. This function of TOE-2 required the DEP domain but not localization to the membrane. We propose that TOE-2 ensures an apoptotic fate for the small Q.a daughter by promoting asymmetry in the daughter cell sizes of the Q.a neuroblast division but by a mechanism that is independent of cell size in the Q.p division.
Annotating Modal Expressions in the Chinese Treebank

This paper reports an effort to annotate modality in the Penn Chinese Treebank. We introduce the modals and features that were annotated, and describe the phases of our working process. Along with this, we address the issues in the preparation of annotation guidelines, and present the preliminary results of the first pass. Finally, we analyze the types of disagreement, and propose directions to improve consistency.
A feedback constraint optimization method for intensity-modulated radiation therapy of nasopharyngeal carcinoma

Intensity-modulated radiation therapy (IMRT) is able to achieve good target conformance with a limited dose to organs at risk (OARs); however, IMRT increases the irradiation volume and monitor units (MUs) required. The present study aimed to evaluate the use of an IMRT plan with fewer segments and MUs, while maintaining quality in the treatment of nasopharyngeal carcinoma. In the present study, two types of IMRT plan were therefore compared: The direct machine parameter optimization (DMPO)-RT method and the feedback constraint DMPO-RT (fc_DMPO-RT) method, which utilizes compensative feedback constraint in DMPO-RT and maintains optimization. Plans for 23 patients were developed with identical dose prescriptions. Each plan involved synchronous delivery to various targets, with identical OAR constraints, by means of 7 coplanar fields. The average dose, maximum dose, dose-volume histograms of targets and the OAR, MUs of the plan, the number of segments, delivery time and accuracy were subsequently compared. The fc_DMPO-RT exhibited superior dose distribution in terms of the average, maximum and minimum doses to the gross tumor volume compared with that of DMPO-RT (t=62.7, 20.5 and 22.0, respectively; P<0.05). The fc_DMPO-RT also resulted in a smaller maximum dose to the spinal cord (t=7.3; P<0.05), as well as fewer MUs, fewer segments and decreased treatment times than that of the DMPO-RT (t=6.2, 393.4 and 244.3, respectively; P<0.05). The fc_DMPO-RT maintained plan quality with fewer segments and MUs, and the treatment time was significantly reduced, thereby resulting in reduced radiation leakage and an enhanced curative effect. Therefore, introducing feedback constraint into DMPO may result in improved IMRT planning. In nasopharyngeal carcinoma specifically, feedback constraint resulted in the improved protection of OARs in proximity of targets (such as the brainstem and parotid) due to sharp dose distribution and reduced MUs.
Is Silence Golden in Human-Robot Dialogue?

The physical actions performed by any robot can be used to convey meaning to a user in human-robot interaction. For example, successfully performing an action following a request may be viewed as an acceptance, while performing the wrong action may be construed as a mis-understanding. Even hesitating to perform a requested physical action may be viewed as a signal of non-understanding. Thus, unlike in the more orthodox domain of non-situated dialogue, natural human-robot dialogue must account for physical actions as a natural and effective implicit communication channel. Though physical actions have not always been explicitly accounted for in dialogue act annotation schemes and models, e.g., vanilla DAMSL lacks a direct mechanism for such implicit communication (Allen and Core 1997), the nature of physical actions as a type of communicative act has been long recognized within the dialogue community (see for example Coulthard & Brazil (1979) for an early account). Indeed, the physical performance of an action can be regarded as a variant on multi-modal interaction (Pfleger, Alexandersson, and Becker 2003). However, while the analysis of physical actions as communicative acts is not new, it is less clear how dialogue planning policies for human-robot interaction should be influenced by the co-occurrence of physical tasks actions. Addressing this issue successfully inevitably depends on knowing whether users consider verbal communication acts alongside physical acts to be superficial or unnatural, and on whether explicit verbal acts can be beneficial given the limitations of imperfect communication. With these questions in mind, in the following we report on a recently conducted study with an implemented humanrobot dialogue system which was designed to assess the importance of compounded physical and verbal communicative acts in human-robot dialogue.
Mass Digitization of Archival Documents using Mobile Phones

Digital copies of historical documents are needed for the Digital Humanities. Currently, cameras of standard mobile phones are able to capture documents with a resolution of about 330 dpi for document sizes up to DIN A4 (German standard, 297 x 210 mm), which allows a digitization of documents using a standard device. Thus, scholars are able to take images of documents in archives themselves without the need of book scanners or other devices. This paper presents a scanning app, which comprises a real time page detection, quality assessment (focus measure) and an automated detection of a page turn over if books are scanned. Additionally, a portable device - the ScanTent - to place the mobile phone during scanning is presented. The page detection is evaluated on the ICDAR2015 SmartDoc competition dataset and shows a reliable page detection with an average Jaccard index of 75%.
An Iterative Approach to Synthesize Data Transformation Programs

Programming-by-Example approaches allow users to transform data by simply entering the target data. However, current methods do not scale well to complicated examples, where there are many examples or the examples are long. In this paper, we present an approach that exploits the fact that users iteratively provide examples. It reuses the previous subprograms to improve the efficiency in generating new programs. We evaluated the approach with a variety of transformation scenarios. The results show that the approach significantly reduces the time used to generate the transformation programs, especially in complicated scenarios.