Miracle-dz/UniFAR-FTUs huggingface dataset:
Eco-friendly fluorimetric approaches for the simultaneous estimation of the co-administered ternary mixture: etoposide, moxifloxacin and nalbuphine

Antineoplastic drugs, etoposide (ETO), are widely used in leukaemia. A patient with leukaemia has a relative infection with pneumonia treated by fluoroquinolones as moxifloxacin HCL (MOX). Because opioid analgesic as nalbuphine HCL (NAL) does not have a ceiling dose, it is used to manage the distasteful sensory in leukaemia. Consequently, green methods for synchronous spectrofluorimetric quantification of a ternary mixture of ETO, MOX and NAL were developed. The first approach relies simply on the estimation of MOX at 371 nm by conventional synchronous fluorimetric technique (Δλ of 60 nm). The second approach depends on applying the first derivative synchronous fluorimetric technique (Δλ of 60 nm) for simultaneous estimation of ETO and NAL at 257 and 273 nm, respectively. A good linear correlation was obtained in the ranges of 0.04–0.40, 0.10–1.00 and 0.50–5.00 µg ml−1 for MOX, ETO and NAL, respectively. Moreover, the proposed approaches were successfully applied for the estimation of the studied drugs in the pharmaceutical dosage forms. Additionally, the synchronous assessment of ETO, MOX and NAL in the spiked human urine was successfully attained by the facile protein precipitation technique. The mean % recoveries in spiked human urine were 99.49, 98.07 and 98.48 for MOX, ETO and NAL, respectively.
Niche shifts after island colonization spurred adaptive diversification and speciation in a cosmopolitan bird clade

Islands have long been recognized as key contributors to biodiversity because they facilitate geographic isolation and ecological divergence from mainland ancestors. However, island colonization has traditionally been considered an evolutionary dead-end process, and its consequences for continental biodiversity remain understudied. Here, we use the evolutionary radiation of Columbiformes (i.e. pigeons and doves) to examine if ecological niche shifts on islands shaped biological diversification and community composition on continents. We show that the colonization of islands by continental, terrestrial-foraging lineages led to the exploitation of a new ecological niche (i.e. arboreal foraging). This transition towards arboreal foraging was associated with evolutionary adaptation towards a new morphological optimum. In addition, arboreal-foraging lineages of islands experienced an increase in speciation rates, which was associated with successful range expansions to other islands as well as back colonization of continents. Our results provide empirical evidence that diversification on continents can only be fully understood when studying the diversification processes that took place on islands, challenging the view of islands as mere sinks of evolutionary diversity.
The effect of survivin gene in breast cancer risk and prognosis

Abstract Objectives The accumulation of genetic damages in onset of cancer induce activation of protooncogenes or inactivation of tumor suppressor genes thus cause disruption of the balance between cell proliferation and programmed cell death. As a member of the apoptosis inhibitory protein family (IAP), survivin play important roles in carcinogenesis process. The evidence suggests that polymorphisms located in survivin promoter region may be important in determining genetic susceptibility of cancer. In this study, we aimed to examine a possible role of survivin −31 and −625 G/C gene polymorphisms in breast cancer. Methods A total of 160 breast cancer cases and 153 healthy controls were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methodology. Results Genotype and allele distributions and of −31 and −625 G/C polymorphisms were not significantly different between two groups. However, we observed the carriers of survivin −625 C/G polymorphism homozygous genotypes (GG/CC) were the significantly higher in patients with tumor necrosis (p=0.047). Conclusions Our results suggest that survivin −625 C/G polymorphism may be related with tumor prognosis, but we are opinion of that our result require to be validated in larger samples and further comprehensive research may explore the correlation.
Preparation of cellulose nanocrystals from empty fruit bunch of palm oil by using phosphotungstic acid

Empty fruit bunch (EFB) of palm oil, an abundant agro-waste in Indonesia, was used as raw material of Cellulose Nanocrystals (CNCs) preparation. Instead of conventional acid mineral, phosphotungstic acid (H3PW12O40, HPW) was used to hydrolyze cellulose due to recycling ability and easy handling. Before hydrolysis process, dried EFB was treated by 3% NaOH solution at 90°C for 2 hours and then bleached using 2% NaClO2 solution at 80°C for 3 hours to remove hemicellulose and lignin. Hydrolysis reaction parameters such as temperature, acid concentration, and reaction time were optimized with fixed solid-liquid ratio of 1:40. Response surface method was used for experimental design to determine the optimum condition of each parameter by using software Minitab. In this study, pulp from dried EFB produced 44.8% yield of CNCs. Dynamic Light Scattering (DLS) analysis showed that most of CNCs equivalent diameter was 140 nm. Crystallinity index was observed at 73.3% using X-ray Diffraction (XRD) analysis. Thus, a green established process for the preparation of CNCs was achieved.
Experimental ﬁ ller design in ﬂ uences error correction rates in a word restoration paradigm

: Including fillers or distractors in psycholinguistic experiments has been standard for decades; yet, relatively little is known how the design of these items interacts with critical manipulations. In this paper, we ask about the role that contextual statistical information in filler items plays in determining if and how to correct a given error, and how grammatical expectations interact with context. We first replicate a speech restoration experiment conducted by Mack, J. E. , C. Clifton, L. Frazier & P. V. Taylor. 2012. (Not) hearing optional subjects: The effects of pragmatic usage preferences. Journal of Memory and Language 67. 211 – 223, measuring usage preferences of null-subject constructions. Then we report two additional experiments in which we manipulated only the ﬁ ller items, either having noise appear uniformly at random, or with a particular bias. Our results (1) demonstrate that listeners are sensitive to statistical patterns in the distribution of noise within the experiment, and (2) suggest that this paradigm can be used to investigate interaction between the mechanisms that govern grammatical preferences, and those that govern error correction processes.
Tailored extracellular electron transfer pathways enhance the electroactivity of Escherichia coli

Extracellular electron transfer (EET) engineering in Escherichia coli holds great potential for bioremediation, energy and electrosynthesis applications fueled by readily available organic substrates. Due to its vast metabolic capabilities and availability of synthetic biology tools to adapt strains to specific applications, E. coli is of advantage over native exoelectrogens, but limited in electron transfer rates. We enhanced EET in engineered strains through systematic expression of electron transfer pathways differing in cytochrome composition, localization and origin. While a hybrid pathway harboring components of an E. coli nitrate reductase and the Mtr complex from the exoelectrogen Shewanella oneidensis MR-1 enhanced EET, the highest efficiency was achieved by implementing the complete Mtr pathway from S. oneidensis MR1 in E. coli. We show periplasmic electron shuttling through overexpression of a small tetraheme cytochrome to be central to the electroactivity of this strain, leading to enhanced degradation of the pollutant methyl orange and significantly increased electrical current to graphite electrodes.
Incremental SCC Maintenance in Sparse Graphs

In the incremental cycle detection problem, edges are added to a directed graph (initially empty), and the algorithm has to report the presence of the first cycle, once it is formed. A closely related problem is the incremental topological sort problem, where edges are added to an acyclic graph, and the algorithm is required to maintain a valid topological ordering. Since these problems arise naturally in many applications such as scheduling tasks, pointer analysis, and circuit evaluation, they have been studied extensively in the last three decades. Motivated by the fact that in many of these applications, the presence of a cycle is not fatal, we study a generalization of these problems, incremental maintenance of strongly connected components (incremental SCC). Several incremental algorithms in the literature which do cycle detection and topological sort in directed acyclic graphs, such as those by [7] and [16], also generalize to maintain strongly connected components and their topological sort in general directed graphs. The algorithms of [16] and [7] have a total update time of O ( m 3 / 2 ) and O ( m · min { m 1 / 2 , n 2 / 3 } ) respectively, and this is the state of the art for incremental SCC. But the most recent algorithms for incremental cycle detection and topological sort ([8] and [10]), which yield total (randomized) update time ˜ O (min { m 4 / 3 , n 2 } ), do not extend to incremental SCC. Thus, there is a gap between the best known algorithms for these two closely related problems. In this paper, we bridge this gap by extending the framework of [10] to general directed graphs. More concretely, we give a Las Vegas algorithm for incremental SCCs with an expected total update time of ˜ O ( m 4 / 3 ). A key ingredient in the algorithm of [10] is a structural theorem (first introduced in [8]) that bounds the number of “equivalent” vertices. Unfortunately, this theorem only applies to
Finding an Approximate Mode of a Kernel Density Estimate

Given points P = { p 1 , . , p n } subset of R d , how do we find a point x which approximately maximizes the function 1 n P p i ∈ P e −∥ p i − x ∥ 2 ? In other words, how do we find an approximate mode of a Gaussian kernel density estimate (KDE) of P ? Given the power of KDEs in representing probability distributions and other continuous functions, the basic mode finding problem is widely applicable. However, it is poorly understood algorithmically. We provide fast and provably accurate approximation algorithms for mode finding in both the low and high dimensional settings. For low (constant) dimension, our main contribution is a reduction to solving systems of polynomial inequalities. For high dimension, we prove the first dimensionality reduction result for KDE mode finding. The latter result leverages Johnson-Lindenstrauss projection, Kirszbraun’s classic extension theorem, and perhaps surprisingly, the mean-shift heuristic for mode finding. For constant approximation factor these algorithms run in O ( n (log n ) O ( d ) ) and O ( nd + (log n ) O (log 3 n ) ), respectively; these are proven more precisely as a (1 + ϵ )-approximation guarantee. Furthermore, for the special case of d = 2, we give a combinatorial algorithm running in O ( n log 2 n ) time. We empirically demonstrate that the random projection approach and the 2-dimensional algorithm improves over the state-of-the-art mode-finding heuristics.
Single-embryo phosphoproteomics reveals the importance of intrinsic disorder in cell cycle dynamics

Switch-like cyclin-dependent kinase (CDK)-1 activation is thought to underlie the abruptness of mitotic onset, but how CDKs can simultaneously phosphorylate many diverse substrates is unknown, and direct evidence for such phosphorylation dynamics in vivo is lacking. Here, we analysed protein phosphorylation states in single Xenopus embryos throughout synchronous cell cycles. Over a thousand phosphosites were dynamic in vivo, and assignment of cell cycle phases using egg extracts revealed hundreds of S-phase phosphorylations. Targeted phosphoproteomics in single embryos showed switch-like mitotic phosphorylation of diverse protein complexes. The majority of cell cycle-regulated phosphosites occurred in CDK consensus motifs, and 72% located to intrinsically disordered regions. Dynamically phosphorylated proteins, and documented substrates of cell cycle kinases, are significantly more disordered than phosphoproteins in general. Furthermore, 30-50% are components of membraneless organelles. Our results suggest that phosphorylation of intrinsically disordered proteins by cell cycle kinases, particularly CDKs, allows switch-like mitotic cellular reorganisation.
Pyruvate:ferredoxin oxidoreductase and low abundant ferredoxins support aerobic photomixotrophic growth in cyanobacteria

The decarboxylation of pyruvate is a central reaction in the carbon metabolism of all organisms. Both the pyruvate:ferredoxin oxidoreductase (PFOR) and the pyruvate dehydrogenase (PDH) complex catalyze this reaction. Whereas PFOR reduces ferredoxin, the PDH complex utilizes NAD+. Anaerobes rely on PFOR, which was replaced during evolution by the PDH complex found in aerobes. Cyanobacteria possess both. Our data challenge the view that PFOR is exclusively utilized for fermentation. Instead, we show, that the cyanobacterial PFOR is stable in the presence of oxygen in vitro and is required for optimal photomixotrophic growth under aerobic conditions while the PDH complex is inactivated under the same conditions. We found that cells rely on a general shift from utilizing NAD(H)-dependent to ferredoxin-dependent enzymes under these conditions. The utilization of ferredoxins instead of NAD(H) saves a greater share of the Gibbs free energy, instead of wasting it as heat. This obviously simultaneously decelerates metabolic reactions as they operate closer to their thermodynamic equilibrium. It is common thought that during evolution, ferredoxins were replaced by NAD(P)H due to their higher stability in an oxidizing atmosphere. However, utilization of NAD(P)H could also have been favored due to a higher competitiveness because of an accelerated metabolism.
Influence of substrate movement on the ITO film thickness distribution during magnetron sputtering

In this paper, the influence of the translational/rotational movement of the substrate on the thickness distribution of the deposited indium tin oxide (ITO) layer during magnetron sputtering is studied. The ITO films were fabricated in a sputtering system equipped with a circular planar magnetron and then compared with the calculated deposition profiles. For the latter purpose, the distribution of emitted particles appear to be successfully described by the cosinelike (Lambert–Knudsen) law. The comparison results indicate that the presence of the substrate motion is equivalent to the change of the deposition angle in a nonlinear manner controlled by the ratio between the substrate and the effective sputtering velocities. The complete reproduction of the measurement results of the calculations confirms validity of the approach. The study findings provide a distinctive way to predict the film thickness distribution and allow to design a restrictive shield to improve film uniformity in planar magnetron sputt.
Online Tools for Teaching Cancer Bioinformatics

The rise of deep molecular characterization with omics data as a standard in biological sciences has highlighted a need for expanded instruction in bioinformatics curricula. Many large biology data sets are publicly available and offer an incredible opportunity for educators to help students explore biological phenomena with computational tools, including data manipulation, visualization, and statistical assessment. ABSTRACT The rise of deep molecular characterization with omics data as a standard in biological sciences has highlighted a need for expanded instruction in bioinformatics curricula. Many large biology data sets are publicly available and offer an incredible opportunity for educators to help students explore biological phenomena with computational tools, including data manipulation, visualization, and statistical assessment. However, logistical barriers to data access and integration often complicate their use in undergraduate education. Here, we present a cancer bioinformatics module that is designed to overcome these barriers through six exercises containing authentic, biologically motivated computational exercises that demonstrate how modern omics data are used in precision oncology. Upper-division undergraduate students develop advanced Python programming and data analysis skills with real-world oncology data which integrates proteomics and genomics. The module is publicly available and open source at https://paynelab.github. io/biograder/bio462. These hands-on activities include explanatory text, code demonstrations, and practice problems and are ready to implement in bioinformatics courses.
A unique yet technically simple type of joint allows for the high mobility of scorpion tails

Although being one of the most well-known animal groups, functional and constructional aspects of scorpions and especially of their tail (metasoma) have so far been overlooked. This tail represents a special construction, as it consists of five tube-shaped segments made up of strong cuticle, which are movable against each other and thus manoeuvre the notorious stinger both quickly and very precisely in space. This high mobility of an exoskeletal structure can be attributed to the connection between the segments described here for the first time. This joint allows for the twisting and bending at the same time in a single, simple construction: adjoining metasomal segments each possess an almost circular opening posteriorly, where the next segment is lodged. Anteriorly, these segments possess two saddle-like protrusions laterally, which are able to rotate in two directions on the rim of the posterior circular opening of the previous segment allowing for twisting and bending. The metasomal joint is particularly noteworthy since its mechanism can be compared to that of arthropod appendages. The scorpion metasoma is actually the only known case in Chelicerata, in which an entire body section has been modified to perform tasks similar to that of an appendage while containing digestive organs. The joint mechanism can also inspire technical applications, for instance in robotics.
Let’s not put a label on it: right-wing terrorism in the news

ABSTRACT Media portrayals of terrorism, particularly right-wing terrorism, have been understudied. In response, this study focuses on understanding how right-wing terrorism is portrayed by the New York Times and the Washington Post. A qualitative content analysis was conducted on five cases. Framing theory and thematic analysis were used to inform the research methods. Four main themes emerge: “officially, we cannot be sure this was terrorism”; “just a man – the obfuscation of motive”; “on normalisation and humanisation”; and “eventually we have to talk about gun policy. ” The results show that the news providers did not label these cases as terrorism, and that the ideology of the attackers was minimised as a motive. By searching so extensively for “other reasons” for the violence, the threat of right-wing violence was minimised. As a result of these incomplete or misleading portrayals, the threat from these individuals goes unchecked.
Recommending Search Queries in Documents Using Inter N-Gram Similarities

Reading a document can often trigger a need for additional information. For example, a reader of a news article might be interested in information about the persons and events mentioned in the article. Accordingly, there is a line of work on recommending search-engine queries given a document read by a user. Often, the recommended queries are selected from a query log independently of each other, and are presented to the user without any context. We address a novel query recommendation task where the recommended queries must be n-grams (sequences of consecutive terms) in the document. Furthermore, inspired by work on using inter-document similarities for document retrieval, we explore the merits of using inter n-gram similarities for query recommendation. Specifically, we use a supervised approach to learn an inter n-gram similarity measure where the goal is that n-grams that are likely to serve as queries will be deemed more similar to each other than to other n-grams. We use the similarity measure in a wide variety of query recommendation approaches which we devise as adaptations of ad hoc document retrieval techniques. Empirical evaluation performed using data gathered from Yahoo! 's search engine logs attests to the effectiveness of the resultant recommendation methods.
Stability Yields Sublinear Time Algorithms for Geometric Optimization in Machine Learning

In this paper, we study several important geometric optimization problems arising in machine learning. First, we revisit the Minimum Enclosing Ball (MEB) problem in Euclidean space R d . The problem has been extensively studied before, but real-world machine learning tasks often need to handle large-scale datasets so that we cannot even afford linear time algorithms. Motivated by the recent developments on beyond worst-case analysis, we introduce the notion of stability for MEB, which is natural and easy to understand. Roughly speaking, an instance of MEB is stable, if the radius of the resulting ball cannot be significantly reduced by removing a small fraction of the input points. Under the stability assumption, we present two sampling algorithms for computing radius-approximate MEB with sample complexities independent of the number of input points n . In particular, the second algorithm has the sample complexity even independent of the dimensionality d . We also consider the general case without the stability assumption. We present a hybrid algorithm that can output either a radius-approximate MEB or a covering-approximate MEB, which improves the running time and the number of passes for the previous sublinear MEB algorithms. Further, we extend our proposed notion of stability and design sublinear time algorithms for other geometric optimization problems including MEB with outliers, polytope distance, one-class and two-class linear SVMs (without or with outliers). Our proposed algorithms also work fine for kernels.
Center Effects: Counseling Center Variables as Predictors of Psychotherapy Outcomes

Treatment context may have a unique impact on psychotherapy outcomes, above and beyond client, therapist, and therapy process variables. University counseling centers represent one such treatment context facing increasing treatment demands. This study examined the role of counseling centers and center variables in explaining differences in psychotherapy outcomes. The Center for Collegiate Mental Health, a large practice–research network, contained data from 116 counseling centers, 2,362 therapists, and 58,423 clients. Multilevel modeling tested if some counseling centers systematically achieved better outcomes than others (a “center effect”). Outcome was operationalized as clients’ magnitude and rate of change in distress across treatment. Results showed a relatively small “center effect” for both outcomes. Analyses sought to explain that center effect through administrative policies and characteristics. As a group, these variables partially explained the center effect. None explained a large portion of total outcome variance. Potential future implications for policy and advocacy efforts are discussed.