Miracle-dz/UniFAR-FTUs huggingface dataset:
Promoter boundaries for the luxCDABE and betIBA-proXWV operons in Vibrio harveyi defined by the method RAIL: Rapid Arbitrary PCR Insertion Libraries

Experimental studies of transcriptional regulation in bacteria require the ability to precisely measure changes in gene expression, often accomplished through the use of reporter genes. However, the boundaries of promoter sequences required for transcription are often unknown, thus complicating construction of reporters and genetic analysis of transcriptional regulation. Here, we analyze reporter libraries to define the promoter boundaries of the luxCDABE bioluminescence operon and the betIBA-proXWV osmotic stress operon in Vibrio harveyi. We describe a new method called RAIL (Rapid Arbitrary PCR Insertion Libraries) that combines the power of arbitrary PCR and isothermal DNA assembly to rapidly clone promoter fragments of various lengths upstream of reporter genes to generate large libraries. To demonstrate the versatility and efficiency of RAIL, we analyzed the promoters driving expression of the luxCDABE and betIBA-proXWV operons and created libraries of DNA fragments from these loci fused to fluorescent reporters. Using flow cytometry sorting and deep sequencing, we identified the DNA regions necessary and sufficient for maximum gene expression for each promoter. These analyses uncovered previously unknown regulatory sequences and validated known transcription factor binding sites. We applied this high-throughput method to gfp, mCherry, and lacZ reporters and multiple promoters in V. harveyi. We anticipate that the RAIL method will be easily applicable to other model systems for genetic, molecular, and cell biological applications. Importance Gene reporter constructs have long been essential tools for studying gene regulation in bacteria, particularly following the recent advent of fluorescent gene reporters. We developed a new method that enables efficient construction of promoter fusions to reporter genes to study gene regulation. We demonstrate the versatility of this technique in the model bacterium Vibrio harveyi by constructing promoter libraries for three bacterial promoters using three reporter genes. These libraries can be used to determine the DNA sequences required for gene expression, revealing regulatory elements in promoters. This method is applicable to various model systems and reporter genes for assaying gene expression.
A Synthetic Microbial Operational Amplifier

Synthetic biology has created oscillators, latches, logic gates, logarithmically linear circuits, and load drivers that have electronic analogs in living cells. The ubiquitous operational amplifier, which allows circuits to operate robustly and precisely has not been built with bio-molecular parts. As in electronics, a biological operational-amplifier could greatly improve the predictability of circuits despite noise and variability, a problem that all cellular circuits face. Here, we show how to create a synthetic 3-stage inducer-input operational amplifier with a differential transcription-factor stage, a CRISPR-based push-pull stage, and an enzymatic output stage with just 5 proteins including dCas9. Our ‘Bio-OpAmp’ expands the toolkit of fundamental circuits available to bioengineers or biologists, and may shed insight into biological systems that require robust and precise molecular homeostasis and regulation. One Sentence Summary A synthetic bio-molecular operational amplifier that can enable robust, precise, and programmable homeostasis and regulation in living cells with just 5 protein parts is described.
Control and the Analysis of Cancer Growth Models

In this note, we analyze two cancer dynamical models from a system-theoretic point of view. The first model is based upon stochastic controlled versions of the classical Lotka-Volterra equations. Here we consider from a controls point of view the utility of employing ultrahigh dose flashes in radiotherapy. The second is based on work of Norton-Simon-Massagué growth model that takes into account the heterogeneity of a tumor cell population. We indicate an optimal strategy based on linear quadratic control applied to a linear transformed model.
A Natural Language Interface to a Database System

Two Natural Language Interface to Database (NLIDB) systems have been developed. One is using a Template Grammar based approach and another is using Keyword based approach. Both the systems accept queries in Bengali language. In both the approaches, the user query is analyzed and translated to a SQL statement that is used to retrieve information from the database. The systems have been evaluated based on precision and recall metrics. The NLIDB system based on Keyword based approach has been observed to perform better. The Keyword based approach has been extended further to develop a dialogue based question answering system for Railway information in Telugu language.
Phylofactorization: a graph-partitioning algorithm to identify phylogenetic scales of ecological data

The problem of pattern and scale is a central challenge in ecology [27]. The problem of scale is central to community ecology, where functional ecological groups are aggregated and treated as a unit underlying an ecological pattern, such as aggregation of “nitrogen fixing trees” into a total abundance of a trait underlying ecosystem physiology. With the emergence of massive community ecological datasets, from microbiomes to breeding bird surveys, there is a need to objectively identify the scales of organization pertaining to well-defined patterns in community ecological data. The phylogeny is a scaffold for identifying key phylogenetic scales associated with macroscopic patterns. Phylofactorization was developed to objectively identify phylogenetic scales underlying patterns in relative abundance data. However, many ecological data, such as presence-absences and counts, are not relative abundances, yet the logic of defining phylogenetic scales underlying a pattern of interest is still applicable. Here, we generalize phylofactorization beyond relative abundances to a graph-partitioning algorithm for traits and community-ecological data from any exponential-family distribution. Generalizing phylofactorization yields many tools for analyzing community ecological data. In the context of generalized phylofactorization, we identify three phylogenetic factors of mammalian body mass which arose during the K-Pg extinction event, consistent with other analyses of mammalian body mass evolution. We introduce a phylogenetic analysis of variance which refines our understanding of the major sources of variation in the human gut. We employ generalized additive modeling of microbes in central park soils to confirm that a large clade of Acidobacteria thrive in neutral soils. We demonstrate how to extend phylofactorization to generalized linear and additive modeling of any dataset of exponential family random variables. We finish with a discussion of how phylofactorization produces a novel species concept, a hybrid of a phy-logenetic and ecological species concepts in which the phylogenetic scales and units of interest are defined objectively by defining the ecological pattern and partitioning the phylogeny into clades based on different contributions to the pattern. All of these tools can be implemented with a new R package available online.
Multi-label image categorization for general concepts using bag of words model

This thesis presents a framework for automatic image categorization for general concepts using bag of words model. We use Lowe’s DoG (Difference of Gaussians) detector to extract image features and represent these local patches by SIFT (Scaleinvariant feature transform) descriptor. Since the size of our image database, the dimensionality of features as well as the codebook sizes needed in the experiments are quite large we implement BIRCH (Balanced iterative reducing and clustering) clustering method, which is firstly proposed by Tian Zhang and widely used in the data mining area, as a possible substitution to the k-means algorithm in the codebook generation procedure. Compared with traditional k-means, although BIRCH clustering is of high efficiency and with arbitrary low memory cost, the evaluation results show it still cannot replace k-means as the method to generate codebooks. In learning and recognition procedure, we use Support vector machines (SVMs) to train classifiers. Two models of MODEL-n and MODEL-x are evaluated and compared in the multilabel image classification. Although correlation information between different labels can be used in MODEL-n. MODEL-x is still better as for the class discrimination ability. To improve the image categorization of the classifiers, codebook combination method is proposed in this thesis. The result shows that the classification performance can be improved for most combinations. As for the optimal combination, it normally appears when combining the codebook with the highest F-measuremac and a small size codebook with the comparatively coarse codewords. In our experiment, the F-measuremac of the best combination of MODEL-n and MODEL-x can be increase by 8.7% and 1.9% compared with that of the best single codebooks. For the problem of handling class imbalance, cost-sensitive method is adopted. We add a new coefficient β to the cost equations and use grid search to get the optimal penalty values for different classes. The F-measuremac of the codebook we use in the experiment is increased by 21.8%. Thesis Supervisor: Dr. Michael S. Lew
Detection of congestive heart failures using C4.5 Decision Tree

Automatic electrocardiogram (ECG) heart beat classification is significant for diagnosis of heart failures. The purpose of this study is to evaluate the effect of C4.5 decision tree method in creating the model that will detect and separate normal and congestive heart failures (CHF) on the long-term ECG time series. The research was conducted in two stages: feature extraction using autoregressive (AR) module and classification by applying C4.5 decision tree method. The ECG signals were obtained from BIDMC Congestive heart failure database and classified by applying different experiments. The experimental results showed that the proposed method reached 99.86% classification accuracy (sensitivity 99.77%, specificity 99.93%, area under the ROC curve 0.998) and has potential in detecting the congestive heart failures.
Power control leased on bit error rate (BER) measurements

We consider power control for the reverse link of a DS/CDMA system where received powers are to be controlled to achieve specified BERs for individual users, not necessarily the same. Our emphasis is to work with bit error rates (BERs), which are more readily measurable than the signal to interference ratios (SIRs), which received a lot of attention in the literature. The power control algorithm that we propose works without knowledge of the relationship between the BER and the SIR. The convergence of this algorithm is shown for a general class of expressions for the BER encountered in digital communications.
Reasoning about Hyperproperties

The importance of security and reliability of software systems makes formal methods of paramount significance for guaranteeing that a system satisfies a particular specification. Hyperproperties can be seen as an abstract formalization of security policies. Because of this, it is desirable to establish a generic verification methodology for at least the class of security-relevant hyperproperties. Unfortunately, such a generic verification methodology is lacking. This is the main motivation of this dissertation. We observe that most interesting hyperproperties that are relevant in practice come from a class of security-relevant policies, specified using universal and possibly existential quantification on traces, as well as relations on those traces. We formalize such definitions and call them holistic hyperproperties. Then our goal becomes to find a methodology for the verification of holistic hyperproperties. To that end, we explore an incremental, coalgebraic perspective on systems and specifications and as a result we arrive at a different, but related kind of specifications: incremental hyperproperties (essentially coinductive predicates). Given some holistic hyperproperty H, the respective incremental version is called H ′ and its definition naturally gives the notion of an H ′-simulation relation. Such relations enable verification of holistic hyperproperties: finding an H ′-simulation relation on a candidate system implies that the incremental hyperproperty H ′ holds and thus the high-level, holistic hyperproperty H holds for the candidate system. We also introduce techniques that are often helpful in translating holistic hyperproperties into incremental ones. To show that incremental hyperproperties are important in practice, we explore their connection with the most closely related verification technique — via unwinding. To achieve this, we propose a framework for coinductive unwinding of security relevant hyperproperties based on Mantel’s MAKS framework [55] and our work on holistic and incremental hyperproperties. Mantel’s MAKS framework cannot be used directly as it is geared towards reasoning about finite behavior and is thus not suitable to reason about holistic hyperproperties in general. However, our framework has a similar structure to MAKS: coinductive unwinding relations compose (or imply) coinductive Basic Security Predicates, which in turn compose a number of security-
Reactive Oxygen Species and Mitochondrial Homeostasis as Regulators of Stem Cell Fate and Function.

SIGNIFICANCE The precise role and impact of reactive oxygen species (ROS) in stem cells, which are essential for lifelong tissue homeostasis and regeneration, remain of significant interest to the field. The long-term regenerative potential of a stem cell compartment is determined by the delicate balance between quiescence, self-renewal, and differentiation, all of which can be influenced by ROS levels. Recent Advances: The past decade has seen a growing appreciation for the importance of ROS and redox homeostasis in various stem cell compartments, particularly those of hematopoietic, neural, and muscle tissues. In recent years, the importance of proteostasis and mitochondria in relation to stem cell biology and redox homeostasis has garnered considerable interest. CRITICAL ISSUES Here, we explore the reciprocal relationship between ROS and stem cells, with significant emphasis on mitochondria as a core component of redox homeostasis. We discuss how redox signaling, involving cell-fate determining protein kinases and transcription factors, can control stem cell function and fate. We also address the impact of oxidative stress on stem cells, especially oxidative damage of lipids, proteins, and nucleic acids. We further discuss ROS management in stem cells, and present recent evidence supporting the importance of mitochondrial activity and its modulation (via mitochondrial clearance, biogenesis, dynamics, and distribution [i.e., segregation and transfer]) in stem cell redox homeostasis. FUTURE DIRECTIONS Therefore, elucidating the intricate links between mitochondria, cellular metabolism, and redox homeostasis is envisioned to be critical for our understanding of ROS in stem cell biology and its therapeutic relevance in regenerative medicine. Antioxid. Redox Signal. 00, 000-000.
Biological evaluation of a series of thiosemicarbazones targeting the large subunit ribosomal protein eL42 from human 80s ribosomes

Background: Thiosemicarbazones are a family known as excellent chelators of enzyme cofactors or molecules with multiple biological activities including antitumor activity [1,2]. Recent studies by Hountondji’s team has revealed that the large subunit ribosomal protein eL42 (molecular weight of 12 kDa, pHi: 10,59) plays a functional role during the elongation step of translation [3] and is over expressed in most cancers [4-6].
Effects of probiotics on central nervous system functions in humans

Objectives: The Cyberball paradigm is often used to study social stress by exclusion/rejection. We aimed to review the existing neuroimaging literatures in order to provide an overview of the neurophysiological mechanisms of social exclusion. Method: Literature search was conducted to identify neurophysiological studies that investigated effects of social exclusion on neural activity using the Cyberball game and the relevant influential factors on these effects. Results: In total, 42 studies using different neuroimaging methods were considered. Regions of the insula, anterior cingulate cortex, temporal and prefrontal cortex were activated to social exclusion. These neural activities were pronounced at latencies ranging from 200 to 400 ms, and between 400 and 900 ms. Influential factors were identified and categorized as intrinsic and extrinsic factors. Conclusion: An integrated framework describing neural activities under social exclusion in terms of both, temporal and spatial processes is provided. Furthermore, the summary of influential intrinsic and extrinsic factors may help us to understand the diversity of the processes and may guide clinical therapy of stress related disorders.
Performance and carcass characteristics of lambs fed a solution of crude glycerin during feedlot and pre-slaughter lairage

ABSTRACT The objective of this study was to evaluate performance and carcass and meat characteristics of lambs fed a solution of crude glycerin plus water (100 g kg−1 of dry matter) (GLY) during feedlot and pre-slaughter lairage. Data were analyzed as a 2 × 2 factorial (GLY available or not in feedlot and GLY available or not in the slaughterhouse). We evaluated the following treatments (feedlot/slaughterhouse): GLY/GLY, GLY/water, water/GLY, and water/water (control). Lambs fed a balanced diet for 70 days [. ]
Towards a new ophthalmic biology and physiology: the unsuspected intrinsic property of melanin to dissociate the water molecule

Charles Darwin (1809-1882) confessed that it is an absurd idea that vertebrate eye could be evolved through natural selection.1 Darwin ́s eye definition was as an organ consisting of at least two different cell types: photoreceptor and pigment cells; this is the Darwinian prototype. Early organisms, more than 600million years ago, (Mya), evolved primitive photoreceptors capable of signaling light. During the Cambrian explosion (540 Mya), animal body evolving rapidly.2 “The simplest organ which can be called an eye consists of an optic nerve, surrounded by pigment cells and covered by translucent skin, but without any lens or other refractive body” Thereby, since Darwin ́s time, the ever presence of melanin was detected. Planarian species in Japan (Polycelis auricularia) has multiple eyes with one photoreceptor cell and one pigment cell only. The general vertebrate plan of an eye-ball encased in three coats: sclera, choroid, and retina, forming a dark chamber filled with clear fluids under pressure. The cornea, a transparent tissue of varying refractive power, depending of habitat. Within the eye is a lens whose means of accommodation is variable in terms of evolution. The lens is pliable and transparent. Accommodation is obtained by striated ciliary muscles cantilevering from a ring of scleral ossicles to deform the lens, rather by to-and-fro movement as it is in fishes. For binocular vision, there is assistance in convergence by a transversal is muscle which orients the lens nasally. The mechanisms for both accommodation and convergence are newly evolved for reptiles. In biology, nothing makes sense except in light of evolution, resolving eye diseases that afflict the population, therefore, requires that we understand the embryology of the organ itself. If we can understand as are originate the tissues, also can understand how they work, and therefore the mechanisms of health and disease.
Cryptic genetic variation defines the adaptive evolutionary potential of enzymes

Genetic variation among orthologous proteins can cause cryptic phenotypic properties that only manifest in changing environments. Such variation may also impact the evolutionary potential of proteins, but the molecular basis for this remains unclear. Here we perform comparative directed evolution in which four orthologous metallo-β-lactamases were evolved toward a new function. We found that genetic variation between these enzymes resulted in distinct evolutionary outcomes. The ortholog with the lower initial activity reached a 20-fold higher fitness plateau exclusively via increasing catalytic activity. By contrast, the ortholog with the highest initial activity evolved to a less-optimal and phenotypically distinct outcome through changes in expression, oligomerization and activity. We show that the cryptic molecular properties and conformational variation of residues in the initial genotypes cause epistasis, thereby constraining evolutionary outcomes. Our work highlights that understanding the molecular details relating genetic variation to protein functions is essential to predicting the evolution of proteins.
Descending pathways from the lateral accessory lobe and posterior slope in the brain of the silkmoth Bombyx mori

A population of descending neurons connect the brain and thoracic motor cener, playing a critical role in controlling behavior. We examined the anatomical organization of descending neurons (DNs) in the brain of the silkmoth Bombyx mori. Moth pheromone orientation is a good model to investigate the neuronal mechanisms of olfactory behavior. Based on mass staining and single-cell staining, we evaluated the anatomical organization of neurite distribution by DNs in the brain. Dense innervation was observed in the posterior–ventral part of the brain, called the posterior slope (PS). We examined the morphology of DNs innervating the lateral accessory lobe (LAL), which is assumed to be important for moth olfactory behavior. We observed that the LAL DNs also innervate the PS, suggesting the integration of signals from the LAL and PS. We also identified a set of DNs innervating the PS, but not the LAL. These DNs were sensitive to sex pheromones, suggesting a role of the PS in motor control for pheromone orientation. The organization of descending pathways for pheromone orientation is discussed.