Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunoprecipitation combined with microchip capillary gel electrophoresis: Detection and quantification of β‐galactosidase from crude E. coli cell lysate

A sensitive and selective analytical method for the determination and quantification of endogenous β‐galactosidase in crude E. coli cell lysates by immunoprecipitation combined with automated microchip capillary gel electrophoresis (IP‐MCGE) with laser‐induced fluorescence (LIF) detection was developed. Total cell lysates were derivatized minimally with a fluorescence dye, incubated with anti‐β‐galactosidase antibodies, and the antigen/antibody complex was precipitated with protein G‐coated magnetic beads. After capturing the complex, it was eluted from the beads under denaturing conditions and loaded directly onto a multisample microchip for analysis. The effects of antibody selection and the importance of preclearing steps were studied in detail. For quantification, an external calibration through spiking pure β‐galactosidase into E. coli lysate was performed. Recovery rates of immunoprecipitation after spiking experiments and the amount of unknown endogenous β‐galactosidase in E. coli lysates were determined. As proof of principle, E. coli cultures grown on nutrition media with several glucose/lactose ratios were analyzed. Differences in the expression level of β‐galactosidase could be detected and measured with the developed method. Detected amounts of β‐galactosidase in different culture media correlated with the β‐galactosidase activities in these cultures.
Coparenting among lesbian, gay, and heterosexual couples: associations with adopted children's outcomes.

Coparenting is associated with child behavior in families with heterosexual parents, but less is known about coparenting among lesbian- and gay-parent families. Associations were studied among self-reported divisions of labor, coparenting observations, and child adjustment (Mage = 3 years) among 104 adoptive families headed by lesbian, gay, or heterosexual couples. Lesbian and gay couples reported sharing child care, whereas heterosexual couples reported specialization (i.e., mothers did more child care than fathers). Observations confirmed this pattern-lesbian and gay parents participated more equally than heterosexual parents during family interaction. Lesbian couples showed the most supportive and least undermining behavior, whereas gay couples showed the least supportive behavior, and heterosexual couples the most undermining behavior. Overall, supportive coparenting was associated with better child adjustment.
Fix Your Eyes in the Space You Could Reach: Neurons in the Macaque Medial Parietal Cortex Prefer Gaze Positions in Peripersonal Space

Interacting in the peripersonal space requires coordinated arm and eye movements to visual targets in depth. In primates, the medial posterior parietal cortex (PPC) represents a crucial node in the process of visual-to-motor signal transformations. The medial PPC area V6A is a key region engaged in the control of these processes because it jointly processes visual information, eye position and arm movement related signals. However, to date, there is no evidence in the medial PPC of spatial encoding in three dimensions. Here, using single neuron recordings in behaving macaques, we studied the neural signals related to binocular eye position in a task that required the monkeys to perform saccades and fixate targets at different locations in peripersonal and extrapersonal space. A significant proportion of neurons were modulated by both gaze direction and depth, i.e., by the location of the foveated target in 3D space. The population activity of these neurons displayed a strong preference for peripersonal space in a time interval around the saccade that preceded fixation and during fixation as well. This preference for targets within reaching distance during both target capturing and fixation suggests that binocular eye position signals are implemented functionally in V6A to support its role in reaching and grasping.
On the Relationship between Complexity and Entropy for Markov Chains and Regular Languages

Using the past-future mutual information as a measure of complexity, the relation between the complexity and the Shannon entropy is determined analytically for sequences generated by Markov chains and regular languages. It is emphasized that, given an entropy value, there are many possible complexity values, and vice versa; that is, the relationship between complexity and entropy is not one-to-one, but rather many-to-one or one-to-many. It is also emphasized that there are structures in the complexity-versus-entropy plots, and these structures depend on the details of a Markov chain or a regular language grammar.
Heuristics-based query optimisation for SPARQL

Query optimization in RDF Stores is a challenging problem as SPARQL queries typically contain many more joins than equivalent relational plans, and hence lead to a large join order search space. In such cases, cost-based query optimization often is not possible. One practical reason for this is that statistics typically are missing in web scale setting such as the Linked Open Datasets (LOD). The more profound reason is that due to the absence of schematic structure in RDF, join-hit ratio estimation requires complicated forms of correlated join statistics; and currently there are no methods to identify the relevant correlations beforehand. For this reason, the use of good heuristics is essential in SPARQL query optimization, even in the case that are partially used with cost-based statistics (i.e., hybrid query optimization). In this paper we describe a set of useful heuristics for SPARQL query optimizers. We present these in the context of a new Heuristic SPARQL Planner (HSP) that is capable of exploiting the syntactic and the structural variations of the triple patterns in a SPARQL query in order to choose an execution plan without the need of any cost model. For this, we define the variable graph and we show a reduction of the SPARQL query optimization problem to the maximum weight independent set problem. We implemented our planner on top of the MonetDB open source column-store and evaluated its effectiveness against the state-of-the-art RDF-3X engine as well as comparing the plan quality with a relational (SQL) equivalent of the benchmarks.
Antiretroviral-Based HIV-1 Prevention: Antiretroviral Treatment and Pre-Exposure Prophylaxis

Antiretroviral-based HIV-1 prevention strategies – including antiretroviral treatment (ART) to reduce the infectiousness of individuals with HIV-1 and oral and topical pre-exposure prophylaxis (PrEP) for uninfected individuals to prevent HIV-1 acquisition – are the most promising new approaches for decreasing HIV-1 spread. Observational studies among HIV-1 serodiscordant couples have associated ART initiation with a reduction in HIV-1 transmission risk of 80–92%, and a recent randomized trial demonstrated that earlier initiation of ART (that is, at CD4+ T-cell counts between 350 and 550 cells/mm3), in the context of virological monitoring and adherence support, resulted in a 96% reduction in HIV-1 transmission. A number of ongoing and recently-completed clinical trials have assessed the efficacy of PrEP for HIV-1 prevention as pericoitally administered or daily-administered 1% tenofovir gel and daily oral tenofovir disoproxil fumarate (TDF) and combination emtricitabine (FTC)/TDF. Completed studies have demonstrated HIV-1 protection efficacies ranging from 39% to 75%. However, two trials in African women have shown no HIV-1 protection with TDF and FTC/TDF PrEP; the reasons for lack of efficacy in those trials are being investigated. Adherence is likely the key to efficacy of antiretrovirals for HIV-1 prevention, both as ART and PrEP. Critical unanswered questions for successful delivery of antiretroviral-based HIV-1 prevention include how to target ART and PrEP to realize maximum population benefits, whether HIV-1-infected individuals at earlier stages of infection would accept ART to reduce their risk for transmitting HIV-1 and whether highest-risk HIV-1- negative persons would use PrEP, and whether high adherence could be sustained to achieve high effectiveness.
An ecological and historical review of bracken (Pteridium esculentum) in New Zealand, and its cultural significance

New Zealand bracken (Pteridium esculentum) belongs to a group of closely related fern species of near global extent. Pteridium species worldwide are aggressive, highly productive, seral plants, functionally more akin to shrubs than ferns. Their deeply buried starch-rich rhizomes allow them to survive repeated fire and their efficient nutrient uptake permits exploitation of a wide range of soils. They are limited by cool annual temperatures, frost, wind, and shallow, poorly drained and acidic soils. Bracken stands accumulate large amounts of inflammable dead fronds and deep litter and often persist by facilitating fire that removes woody competitors. Bracken was present but not abundant in New Zealand before the arrival of humans. Occasional fire or other disturbances created transient opportunities for it. Rhyolitic volcanic eruptions led to short-lived expansions of bracken, and it briefly became dominant over ash-affected areas of the central North Island after the large AD 186 Taupo Tephra eruption. Andesitic eruptions had limited effects. Bracken became one of the most abundant plants in the country after the arrival of Maori in the 13th century, when massive deforestation affected most of the lowland landscape. The bracken-dominated vegetation that formed in most places immediately after burning gave way with time to fire-maintained mosaics in which bracken dominated on deeper soils and under moist, mild climates. Although Maori relied on bracken rhizome starch as a major element of their diet, food-quality rhizomes were obtained only on deep, moderately fertile soils. The dominance of bracken over very large areas was mainly a result of burning to create open landscapes for access and ease of travel. Bracken remained a troublesome weed through the European pastoral period and well into the 20th century. Bracken has a problematical role in conservation as it can form a persistent, fire-prone, low-diversity cover in drier regions. However, it is an indigenous plant that is effective in preventing erosion and, in wetter areas, it will easily suppress exotic grasses and facilitate regeneration to forest. It should be considered an essential component of landscapes conserved for their historical significance to Maori.
Security in cognitive radio networks: An example using the commercial IEEE 802.22 standard

Security in wireless networks is challenging. Security in cognitive radio networks (CRN) is even more challenging. This is because a CRN consists of cognitive radios (CR) which have many more functions and processes to account for, such as sensing, geolocation, spectrum management, access to the policy database etc. Each of these functions and processes need to be assessed for potential vulnerabilities and security mechanisms need to be provided for protection of not just the secondary users of the spectrum but also the primary users or the incumbents. This paper discusses the potential security vulnerabilities and the remediations for the same in a CRN with an example using a commercial IEEE 802.22 standard. Due to the unique characteristics of the CRs in a CRN, enhanced security mechanisms are required. The security mechanisms in CRN are divided into several security sub-layers which protect non-cognitive as well as cognitive functions of the system and the interactions between the two. This paper describes these security features as incorporated into the IEEE 802.22 standard. It is possible to apply similar security mechanisms for a military CRN.
Relational Annotation of Scientific Medical Corpora A Case Study

In life science and biomedicine much knowledge resides as unstructured information in for instance bibliographic databases. To facilitate searching and categorisation of this information the database entries are annotated with terms or keywords, describing for instance diseases, treatments and anatomy. These annotations are limited to concept level and do not describe relations between terms, for example that a given treatment may be used for a given disease, even if this information is available in both the text and terminologies. In this work we will present a possible approach to extend term annotations with relational information to add another dimension to concept focused annotation schemas. This approach could also be used to highlight implicit information and to structure knowledge.
Controversies: Optic nerve sheath fenestration versus shunt placement for the treatment of idiopathic intracranial hypertension

Background: Idiopathic intracranial hypertension (IIH) has been increasing in prevalence in the past decade, following the obesity epidemic. When medical treatment fails, surgical treatment options must be considered. However, controversy remains as to which surgical procedure is the preferred surgical option – optic nerve sheath fenestration (ONSF) or cerebrospinal fluid (CSF) shunting – for the long-term treatment of this syndrome. Purpose: To provide a clinical update of the pros and cons of ONSF versus shunt placement for the treatment of IIH. Design: This was a retrospective review of the current literature in the English language indexed in PubMed. Methods: The authors conducted a PubMed search using the following terms: Idiopathic IIH, pseudotumor cerebri, ONSF, CSF shunts, vetriculo-peritoneal shunting, and lumbo-peritoneal shunting. The authors included pertinent and significant original articles, review articles, and case reports, which revealed the new aspects and updates in these topics. Results: The treatment of IIH remains controversial and lacks randomized controlled clinical trial data. Treatment of IIH rests with the determination of the severity of IIH-related visual loss and headache. Conclusion: The decision for ONSF versus shunting is somewhat institution and surgeon dependent. ONSF is preferred for patients with visual symptoms whereas shunting is reserved for patients with headache. There are positive and negative aspects of both procedures, and a prospective, randomized, controlled trial is needed (currently underway). This article will hopefully be helpful in allowing the reader to make a more informed decision until that time.
The effect of the addition of ropivacaine or bupivacaine upon pruritus induced by intrathecal fentanyl in labour

Sixty patients in early labour were randomly allocated to one of three groups. The control group received intrathecal fentanyl 25 µg, the ropivacaine group received intrathecal fentanyl 25 µg and ropivacaine 2.5 mg while the bupivacaine group received intrathecal fentanyl 25 µg and bupivacaine 2.5 mg. The incidence of pruritus was 100% in controls, compared with 85% in the ropivacaine group (not significant) and 75% in the bupivacaine group (p = 0.003). The severity of pruritus was significantly less in the ropivacaine (p = 0.006) and bupivacaine (p = 0.001) groups. Most patients developed pruritus by 30 min. Pruritus above the abdomen was not reduced in patients receiving local anaesthetics. There were no significant differences in the mean pain visual analogue score, systolic blood pressure, maternal heart rate and upper level of reduced pin‐prick sensation in the first 30 min. Intrathecal ropivacaine and, more so, intrathecal bupivacaine reduce the incidence and severity of pruritus from intrathecal fentanyl for labour analgesia.
Source Coding and Parallel Routing

We consider a simple communication network model and focus on a single source-destination pair to exploit the interconnection between Source Coding and Parallel Routing. We consider a Distortion Measure that combines signal reconstruction fldelity with network delay and we pose the problem of minimizing this Measure by jointly choosing the Encoder Parameters and the Routing Parameters. We look at single-description coding as well as multiple-description coding and we perform numerical optimization that yields interesting design trade-ofis that are insightful and can be exploited in more realistic environments.
Ancient DNA from South-East Europe Reveals Different Events during Early and Middle Neolithic Influencing the European Genetic Heritage

The importance of the process of Neolithization for the genetic make-up of European populations has been hotly debated, with shifting hypotheses from a demic diffusion (DD) to a cultural diffusion (CD) model. In this regard, ancient DNA data from the Balkan Peninsula, which is an important source of information to assess the process of Neolithization in Europe, is however missing. In the present study we show genetic information on ancient populations of the South-East of Europe. We assessed mtDNA from ten sites from the current territory of Romania, spanning a time-period from the Early Neolithic to the Late Bronze Age. mtDNA data from Early Neolithic farmers of the Starčevo Criş culture in Romania (Cârcea, Gura Baciului and Negrileşti sites), confirm their genetic relationship with those of the LBK culture (Linienbandkeramik Kultur) in Central Europe, and they show little genetic continuity with modern European populations. On the other hand, populations of the Middle-Late Neolithic (Boian, Zau and Gumelniţa cultures), supposedly a second wave of Neolithic migration from Anatolia, had a much stronger effect on the genetic heritage of the European populations. In contrast, we find a smaller contribution of Late Bronze Age migrations to the genetic composition of Europeans. Based on these findings, we propose that permeation of mtDNA lineages from a second wave of Middle-Late Neolithic migration from North-West Anatolia into the Balkan Peninsula and Central Europe represent an important contribution to the genetic shift between Early and Late Neolithic populations in Europe, and consequently to the genetic make-up of modern European populations.
GUI Testing Techniques Evaluation by Designed Experiments

Industry uses different testing techniques for test case generation and execution. But in general no systematic evaluation is performed to identify which technique is better (for instance, to find bugs faster). This paper presents a statistical assessment of two GUI testing techniques, BxT and DH, which are used on Motorola phone applications. These techniques test applications by pressing certain phone keys, from certain screens and during some amount of time. We consider three exploration parameters for each technique in our design and analysis of experiments: Driven determines whether a test case always starts from a single initial state (screen) or set of initial states; KeyProb associates an occurrence probability for SizeTC refers to the number of steps a test can have (a fourth parameter is the Technique itself). As conclusions, we show that BxT is better than DH and the SizeTC and the Technique parameters and the combination Driven*SizeTC have significant effects on the time to find a bug.
Circulating MicroRNAs as Biomarkers of Prostate Cancer: The State of Play

MicroRNAs are key regulators of gene expression and play critical roles in both normal physiology and pathology. Recent research has demonstrated that these molecules are present in body fluids, such as serum, plasma, and urine, and can be readily measured using a variety of techniques. More importantly, emerging evidence suggests that circulating or urine miRNAs are useful indicators of disease. Here, we consider the potential utility of such miRNAs as noninvasive biomarkers of prostate cancer, a disease that would benefit substantially from novel diagnostic and prognostic tools. The studies aimed at identifying diagnostic, prognostic, and/or predictive miRNAs for prostate cancer are summarised and reviewed. Finally, practical considerations that will influence the translation of this recent research into clinical implementation are discussed.
Anatomy and frequency of large pontomesencephalic veins on 3D CT angiograms of the circle of Willis.

BACKGROUND AND PURPOSE The pontomesencephalic veins (PMVs), especially the anterior PMV, are sometimes large enough that they could potentially affect the interpretation of CT angiograms of the circle of Willis. We investigated the frequency and anatomy of visible PMVs on 3D CT angiograms. METHODS CT angiograms of 211 consecutive patients who underwent CT angiography for a variety of clinical indications were evaluated retrospectively. Images evaluated by consensus between two neuroradiologists were maximum intensity projection and volume-rendered 3D CT angaiograms. RESULTS Visible PMVs were present on 3D CT angiograms in 11 (5.2%) of 211 patients. Eight of 11 patients had a visible anterior PMV behind the basilar artery. In four patients, the venous caliber of the anterior PMV was sufficiently large enough to be potentially confused with arterial structures. In one patient, 3D CT angiography revealed a large anterior PMV (approximately 2.6 mm in diameter) in the interpeduncular cistern, which had been mistaken for subarachnoid hemorrhage on a nonenhanced CT scan. Two patients had interpeduncular veins of the anterior PMV draping over the dome of a basilar tip aneurysm. In only one patient was the anterior PMV visible possibly owing to arteriovenous malformation. One patient had visible lateral mesencephalic veins, and four patients had visible transverse pontine veins. In one case, on certain views, the transverse pontine veins appeared to arise from the basilar artery. CONCLUSION Because of their small size, PMVs were seen only infrequently on 3D CT angiograms, but neuroradiologists should be familiar with the normal variants of large PMVs to avoid diagnostic and anatomic confusion.
Promoting Thrombolysis in Acute Ischemic Stroke

Background and Purpose— Thrombolysis with intravenous recombinant tissue plasminogen activator is an effective treatment for acute ischemic stroke, but the number of treatable patients is limited. The PRomoting ACute Thrombolysis in Ischemic StrokE (PRACTISE) trial evaluated the effectiveness of a multidimensional implementation strategy for thrombolysis with intravenous recombinant tissue plasminogen activator in acute ischemic stroke. Methods— The PRACTISE trial was a national multicenter cluster-randomized controlled trial with randomization after pairwise matching. Twelve hospitals, both urban and community, academic and nonacademic, in the Netherlands participated. All patients admitted with stroke within 24 hours from onset of symptoms were registered. The intervention included 5 implementation meetings based on the Breakthrough Series model. The primary outcome was treatment with thrombolysis. Secondary outcomes were admission within 4 hours after onset of symptoms, death or disability at 3 months, and quality of life. Results— Overall 5515 patients were included in the study' 308 patients (12.2%) in the control centers and 393 patients (13.1%) in the intervention centers were treated with thrombolysis (adjusted OR, 1.25; 95% CI, 0.93 to 1.68). Among the 1657 patients with ischemic stroke admitted within 4 hours from onset, 391 (44.5%) of 880 in the intervention centers were treated with thrombolysis and 305 (39.3%) of 777 in the control centers; the adjusted OR for treatment with thrombolysis was 1.58 (95% CI, 1.11 to 2.27). Conclusions— An intensive implementation strategy increases the proportion of patients with acute stroke treated with thrombolysis in real-life settings. An apparently pivotal factor in the improvement of the treatment rate is better application of contraindications for thrombolysis.