Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioorthogonal probes for polo-like kinase 1 imaging and quantification.

A nuclear protein target, polo-like kinase 1 (PLK1) was imaged using a biocompatible bioorthogonal ligation between a specific drug and a fluorescent dye in live cells. Colocalization of the dye and the protein target was confirmed by antibody staining and by expressing a GFP construct of PLK1. The two-step PLK1 imaging procedure was used to quantify PLK1 expression levels in cancer cell lines of various tissue origins.
A Two-Stage Geometric Method for Pruning Unreliable Links in Protein-Protein Networks

Protein-protein interactions (PPIs) play essential roles for determining the outcomes of most of the cellular functions of the cell. Although the experimentally detected high-throughput PPI data promise new opportunities for the study of many biological mechanisms including cellular metabolism and protein functions, experimentally detected PPIs have high levels of false positive rate. Therefore, it is of high practical value to develop novel computational tools for pruning low-confidence PPIs. In this paper, we propose a new geometric approach called Leave-One-Out Logistic Metric Embedding (LOO-LME) for assessing the reliability of interactions. Unlike previous approaches which mainly seek to preserve the noisy topological information of the PPI networks in the embedding space, LOO-LME first transforms the learning task into an equivalent discriminant form, then directly deals with the uncertainty in PPI networks using a leave-one-out-style approach. The experimental results show that LOO-LME substantially outperforms previous methods on PPI assessment problems. LOO-LME could thus facilitate further graph-based studies of PPIs and may help infer their hidden underlying biological knowledge.
Modeling thrombus formation and growth

The paper reviews the state‐of‐the‐art in computational modeling of thrombus formation and growth and related phenomena including platelet margination, activation, adhesion, and embolization. Presently, there is a high degree of empiricism in the modeling of thrombus formation. Based on the experimentally observed physics, the review gives useful strategies for predicting thrombus formation and growth. These include determining blood components involved in atherosclerosis, effective blood viscosity, tissue properties, and methods proposed for boundary conditions. In addition to the guidelines, ongoing research on the effect of shear stress on platelet margination, activation and adhesion, and platelet‐surface interactions are reviewed. Biotechnol. Bioeng. 2017;114: 2154–2172. © 2017 Wiley Periodicals, Inc.
Rapid Fluorescence Ratio Assay for Detecting Changes in Radiosensitivity

Abstract Hofland, I. , Ramakers, B. , Begg, A. C. and Vens, C. Rapid Fluorescence Ratio Assay for Detecting Changes in Radiosensitivity. Radiat. Res. 157, 734–739 (2002). To test modifications in sensitization to radiation or drugs in preclinical studies of cancer therapy, the colony-forming assay is regarded as the gold standard. Because this assay is time consuming, somewhat laborious, and unsuitable for rapid screening, development of other assays is desirable. We describe here an assay based on the detection of enhanced green fluorescence protein (EGFP) with flow cytometry that is particularly suitable for genetic manipulation studies in which the gene of interest is introduced together with EGFP as reporter. It is easily adaptable to other reporters, however, whether naturally fluorescent or requiring immunochemical staining. Cells are irradiated as mixed populations of a known standard cell line (nonfluorescent) together with the genetically manipulated cell line expressing EGFP. Ratios of fluorescent and nonfluorescent cells are measured before treatment and several days after treatment. If the cell populations have equal radiosensitivities, the ratio remains unchanged. Changes in the ratio indicate changes in radiosensitivity. The assay was validated for two situations in which dominant negative peptides inhibiting DNA repair were expressed in A549 human lung cells and affected radiosensitivity.
An activator for pyruvoyl-dependent l-aspartate α-decarboxylase is conserved in a small group of the γ-proteobacteria including Escherichia coli

In bacteria, β‐alanine is formed via the action of l‐aspartate α‐decarboxylase (PanD) which is one of the small class of pyruvoyl‐dependent enzymes. The pyruvoyl cofactor in these enzymes is formed via the intramolecular rearrangement of a serine residue in the peptide backbone leading to chain cleavage and formation of the covalently‐bound cofactor from the serine residue. This reaction was previously thought to be uncatalysed. Here we show that in Escherichia coli, PanD is activated by the putative acetyltransferase YhhK, subsequently termed PanZ. Activation of PanD both in vivo and in vitro is PanZ‐dependent. PanZ binds to PanD, and we demonstrate that a PanZ(N45A) site‐directed mutant is unable to enhance cleavage of the proenzyme PanD despite retaining affinity for PanD. This suggests that the putative acetyltransferases domain of PanZ may be responsible for activation to enhance the processing of PanD. Although panD is conserved among most bacteria, the panZ gene is conserved only in E. coli‐related enterobacterial species including Shigella, Salmonella, Klebsiella and Yersinia. These bacteria are found predominantly in the gut flora where pantothenate is abundant and regulation of PanD by PanZ allows these organisms to closely regulate production of β‐alanine and hence pantothenate in response to metabolic demand.
A dominant‐negative transgene defines a role for p56lck in thymopoiesis.

The lymphocyte‐specific protein tyrosine kinase p56lck participates in T cell signaling through functional interactions with components of the T cell antigen receptor complex and the interleukin‐2 receptor. Additional insight into the function of p56lck has now been obtained through the generation of transgenic animals expressing high levels of a catalytically inactive form of this kinase (p56lckR273). Mice bearing the lckR273 transgene manifested a severe defect in the production of virtually all T lymphocytes. Those exceptional CD3+ cells that escaped the effects of the lckR273 transgene were confined primarily to the T cell subset that expresses gamma/delta T cell receptors. Remarkably, construction of a dose‐response curve for the effects of the lckR273 transgene revealed that developmental arrest of thymocytes occurred at a discrete stage in the normal T cell maturation pathway, corresponding to a point at which thymoblasts ordinarily begin a series of mitotic divisions that result in expansion and maturation. These results suggest that p56lck normally regulates T cell production by metering the replicative potential of immature thymoblasts.
Alanine-EPR dosimetry in remote audits of clinical photon beams

There is a need for multiple independent auditing methods for clinical photon beams, for which alanine-EPR dosimeters could be a candidate. In this thesis we attempt to solve some key questions related to developing the alanine remote audit dosimetry system for traceable measurements at DTU Risø(SSDL): 1. which of the two Co source designs at Risø are better for developing the alanine dosimetry system? 2. What is the energy response for alanine dosimeters in MV-beams, and is there a trend in the response as a function of beam quality? 3. Propose a method in which alanine can be used for remote audits of clinical photon beams at Danish hospitals. Calibration curves of irradiated alanine in the dose-range 1 100 Gy are made for both source designs and they are compared on a number of parameters. We find the open source design to be preferable because of low traceability uncertainty and customizable choice of effective measuring point in the calibration. The energy dependence of alanine dosimeters where found experimentally by MV-irradiations of alanine and Farmer chamber dosimeters, and simulated using the egsNRC software for Monte Carlo simulations of particle transport. The experimental results had relative uncertainties of 1.2%, dominated by the uncertainty in the calculated Farmer chamber kQ values. The uncertainties were too high for detecting a trend beyond a constant dependence in beam quality. The simulated results showed a constant energy dependence of HQ = 0.9961 ± 0.0004 for MV-beams in the reference conditions of the performed experiment, we argue that changes in either the phantom or the effective point of measurement(for alanine dosimeters) could give a different HQ. We describe two possible auditing procedures: a dose-rate audit with traceable relative uncertainty 0.7%, and a dose-distribution audit of the treatment planning system of clinical photon beams. Both procedures are relatively simple to perform and require special made phantoms, that can be mailed as part of the remote audit.
Audio-Based Melody Categorization: Exploring Signal Representations and Evaluation Strategies

Abstract Melody categorization refers to the task of grouping a set of melodies into categories of similar items that originate from the same melodic contour. From a computational perspective, automatic melody categorization is of crucial importance for the automatic organization of databases, as well as for large-scale musicological studies—in particular, in the context of folk music and non-Western music traditions. We investigate methods starting from the raw audio file. For each recording contained in a collection, we extract a pitch sequence representing the main melodic line. We then estimate pairwise similarities and evaluate the discriminative power of the resulting similarity matrix with respect to ground-truth annotations. We propose novel evaluation methodologies, compare melody representations, and explore the potential of our approach in the context of two applications: interstyle and intrastyle categorization of flamenco music and tune-family recognition of folk-song recordings.
Leakage detection for oil pipelines based on Independent Component Analysis

Independent Component Analysis (ICA) technique develops from blind source separation (BSS). Mixed signal under certain conditions can be separated effectively by means of ICA technique. In this paper, the principal theory and algorithm of ICA is introduced, application in signal separation and filtering with ICA is studied in leakage detection for oil pipelines and imitation and field examples are given. The experiments show that signal-to-noise ratio of processed signal was raised obviously. Pressure wave in different running modes were analyzed and wave structure recognition was proposed to judge pipeline condition. Characteristic vectors depicting wave were selected and then mode base was established in limit samples. The test results show reliability and validity of this method.
Development of a user-configurable indoor navigation system for robotic wheelchairs

This chapter presents the development of an indoor navigation system using the quick response code (QR code) for the iRW to reduce the operation load on the wheelchair user. Indoor navigation of the iRW uses the automated guided vehicle (AGV) as the design concept for route planning and motion execution. QR code labels are deployed on the ceiling as the “virtual AGV track”. The user interface and indoor navigation algorithm are implemented as an App in the tablet mounted on the armrest of the iRW. The main feature of this indoor navigation is that the system does not need to store a navigation map of the indoor environment. The performance test result is demonstrated that this indoor navigation system is practical for the home environment.
Subtemporal-Anterior Transtentoral Approach to Middle Cranial Fossa Microsurgical Anatomy

Abstract This study aimed to describe the topography of inferior and external dura mater of the middle cranial fossa through subtemporal–anterior transpetrosal approach and discuss the feasibility of improving the approach. Eight formalin-fixed adult cadaveric heads were studied, with the bones milled away in the lateral triangle region of the petrous bone, Kawase rhombus region, and inner triangle region of the petrous apex. The distances between the targets in these regions, as well as the angles after the dissection of zygomatic arch, were measured, and then the exposed petroclival and retrochiasmatic areas were observed under the microscope. There were significant variations in the distances between targets in the 3 milled regions among the specimens. After the dissection of zygomatic arch, the surgical view got an average increase of 12 degrees. The subtemporal anterior transpetrosal approach, as an improved subtemporal approach, can expose the lesions optimally, causing no injury to the hearing and reducing injuries to temporal lobe. On the other hand, the lateral bone of the petrous parts of the temporal bone is removed so as to improve the view to the retrochiasmatic area and expand the operative field.
A Chemically-Bound Glutathione Sensor Bioinspired by the Defense of Organisms against Heavy Metal Contamination: Optimization of the Immobilization Conditions

The influence of the experimental conditions (glutathione concentration and incubation time and temperature) concerning the covalent immobilization of glutathione via carbodiimide coupling on the behavior of a glutathione modified screen-printed carbon electrode obtained by electrografting is evaluated. The optimized parameters fasten the modification process and improve the performance of the sensor as compared to the usual procedure. This suggests the convenience of a tailored preparation of metal sensors based on metal-binding biomolecules such as glutathione.
Sensitivity of ozone to bromine in the lower stratosphere

Measurements of BrO suggest that inorganic bromine (Bry) at and above the tropopause is 4 to 8 ppt greater than assumed in models used in past ozone trend assessment studies. This additional bromine is likely carried to the stratosphere by short‐lived biogenic compounds and their decomposition products, including tropospheric BrO. Including this additional bromine in an ozone trend simulation increases the computed ozone depletion over the past ∼25 years, leading to better agreement between measured and modeled ozone trends. This additional Bry (assumed constant over time) causes more ozone depletion because associated BrO provides a reaction partner for ClO, which increases due to anthropogenic sources. Enhanced Bry causes photochemical loss of ozone below ∼14 km to change from being controlled by HOx catalytic cycles (primarily HO2+O3) to a situation where loss by the BrO+HO2 cycle is also important.
Gastric neuroendocrine tumors Chapter 1 Overview on Gastric Cancer

Gastric Neuroendocrine Tumors (NET)s are classified on the basis of criteria that are common to all gastrointestinal and pancreatic neuroendocrine neoplasms. Most neuroendocrine neoplasms of the stomach are NETs –well differentiated, nonfunctioning enterochromaffin–like(ECL) cell carcinoids (ECL cell NETs)-arise predominantly in the corpus-fundus region [1]. Three distinct types are recognized :
Second and third harmonic suppression in parallel coupled line filter using sliding coupling

A novel method is presented for 2ed and 3rd harmonic suppression in parallel coupled-line band pass filters. It is based on sliding coupling to improved band-reject characteristics of the filters. Easy design, simple implementation, no change in original filter pass-band and good suppression for second and third harmonics are the most advantage of this method. To validate the proposed method, three sample filters are designed and implemented at 3GHz with about 23% band width. The first has −35dB rejection in second harmonic. The second filter has −35dB and −18dB rejection in second and third harmonic consequently and the last has −25 dB rejection for both second and third harmonics. The insertion loss of all filters is less than 0.6 dB with good agreement with simulation.
Average KR Schedule in Learning of Timing: Influence of Length for Summary Knowledge of Results and Task Complexity

This experiment investigated the influence of length for average Knowledge of Results (KR) and task complexity on learning of timing in a barrier knock-down task. Participants (30 men and 30 women) attempted to press a goal button in 1200 msec. after pressing a start button. The participant was assigned into one of six groups by two tasks (simple and complex) and three feedback groups (100% KR, Average 3, Average 5). The simple and complex tasks required a participant to knock down one or three barriers before pressing a goal button. After a pretest without KR, participants practiced 60 trials of physical practice with one of the three following groups as a practice phase: one given the result of movement time after every trial (100% KR), a second given the average movement time after every third trial (Average 3), a third given the average movement time after every fifth trial (Average 5). Participants then performed a posttest with no-KR and two retention tests, taken 10 min. and 24 hr. after the posttest without KR. Analysis gave several findings. (1) On the complex task, the absolute constant error (|CE|) and the variable error (VE) were less than those on the simple task. (2) The |CE| and the VE of the 100% KR and the Average 3 groups were less than those of the Average 5 group in the practice phase, and the VE of the 100% KR and the Average 3 group were less than those of the Average 5 group on the retention tests. (3) In the practice phase, the |CE| and the VE on Blocks 1 and 2 were higher than on Blocks 5 and 6. (4) On the retention tests, the |CE| of the posttest was less than retention tests 1 and 2. And, the VE of the 100% KR and the Average 3 groups were less than that of the Average 5 group. These results suggest that the average feedback length of three trials and the given feedback information after every trial are advantageous to learning timing on this barrier knock-down task.
Universal newborn hearing screening: A question of evidence

The objective of this paper is to present data on the ages of diagnosis and hearing-aid fitting of children with permanent congenital or early-onset hearing loss who were identified through neonatal hearing screening (NHS) programs or medical referral. Data were collected for 709 children born between 1980 and 2003. Children who were screened were diagnosed significantly earlier (mean 6.3 months) than referred children (mean 39.5 months). For the referred children, the ages of diagnosis and amplification improved over time but remained unacceptably high. In addition, there was an inverse relationship between degree of loss and age of diagnosis, with children with lesser degrees of hearing loss identified later than those with severe to profound hearing loss. These results contribute to the evidence that NHS programs lower the ages of diagnosis and amplification and lead to earlier improved hearing. It is argued that early access to hearing should be the desired primary outcome of NHS. The numerous studies demonstrating improved ages of diagnosis resulting from NHS programs constitute adequate evidence to support these initiatives.
A phase I study of panobinostat (LBH589) in patients with primary myelofibrosis (PMF) and post‐polycythaemia vera/essential thrombocythaemia myelofibrosis (post‐PV/ET MF)

Panobinostat (LBH589), a novel histone deacetylase inhibitor (HDACi), was evaluated in a phase I study of patients with primary myelofibrosis (PMF) and post‐essential thrombocythaemia/polycythaemia vera‐related myelofibrosis (Post‐ET/PV MF). Eighteen patients (PMF 56%; Post‐PV MF 28%; Post‐ET MF 17%) were treated in three cohorts at oral doses of (i) 20, (ii) 30, and (iii) 25 mg three times weekly consecutively. Reversible thrombocytopenia was the dose‐limiting toxicity. Five patients (two in Dose Cohort 1, one in Dose Cohort 2 and two in Dose Cohort 3) received six or more cycles and were evaluable for response assessment. After the sixth cycle, three of these five patients achieved clinical improvement (CI) with 100% reduction in palpable splenomegaly from baseline, and two patients experienced stable disease. Panobinostat therapy was also associated with improvement in the degree of anaemia in two of the five patients. Of the three patients who achieved CI after six cycles, one patient achieved a near complete remission after 15 cycles of treatment and another patient had resolution of marrow fibrosis after 16 cycles. We conclude that panobinostat is a well‐tolerated, clinically active treatment for MF patients, regardless of JAK2 V617F status, and most effective when given at low doses over long periods of time.
Continuous stellate ganglion blockade for reflex sympathetic dystrophy.

eflex sympathetic dystrophy (RSD) is a syndrome comprising burning pain, hyperalgesia, R nd allodynia alone or in combination with vasomotor and dystrophic changes and may be related to peripheral nerve injury (1). Sympathetic blockades are often performed to relieve the symptoms of RSD. Both central sympathetic ganglion blockade using a local anesthetic and Bier block with guanethidine or reserpine have been employed with varying success (2). Such treatments are often performed as a series of sympathetic nerve blocks. The following case describes a new method for the continuous blockade of the cervical sympathetic ganglia in a patient resistant to other forms of treatment.
Predictive Effects of Different Clinical Balance Measures and the Fear of Falling on Falls in Postmenopausal Women Aged 50 Years and Over

Background: Falls among the elderly are associated with a high morbidity and mortality and can involve high-cost medical interventions. The risk of falls often remains undiagnosed until an episode occurs but if the risk is high, preventative measures could be introduced. Objectives: This 6-month prospective study investigated whether different postural clinical measures and fear of falling (FOF) itself can predict future falls in postmenopausal women aged ≥50 years. Methods: 125 postmenopausal women were studied comparing the outcome of fallers vs. non-fallers within the 6-month follow-up study period. Clinical measures, history of falls and FOF data were determined at baseline and the number of falls and FOF were ascertained at the final visit or by telephone interview at 6 months. Results: Of the clinical measures investigated, the Falls Efficacy Scale International (FES-I) >26 points (OR = 7.28, per additional point, 95% CI 2.25–23.61, p = 0.001) and Berg Balance Scale (BBS) ≤52 points (OR = 4.77, per additional point, 95% CI = 1.15–19.82, p = 0.031) performed best in prediction of the future falls. Conclusions: Postmenopausal women aged ≥50 years who had FES-I scores >26 points and BBS ≤52 points should be examined for risk factors of future falls and offered preventative measures.
STRUCTURED VERSUS UNSTRUCTURED REGULATION: ON PROCEDURAL MINDSETS AND THE MECHANISMS OF PRIMING EFFECTS

We propose that two distinct regulatory dynamics may produce social psychological priming effects, but under very different conditions. When engaged in structured regulation, people process information in light of their valued goals, responding to salient situational cues only to the extent that those cues are goal-relevant. By contrast, when engaged in unstructured regulation, people are more tuned to the demands of the present, tailoring their responses to the unique circumstances of the immediate context and evincing a greater openness to responding to salient cues in a cueconsistent manner. We explore construal level as one factor that dictates when people engage in one dynamic versus the other. We also discuss the distinction between traditional priming and mindset priming.