Miracle-dz/UniFAR-FTUs huggingface dataset:
Coordination of kinesin's two heads studied with mutant heterodimers

A conventional kinesin molecule has two identical catalytic domains (heads) and is thought to use them alternately to move processively, with 8-nm steps. To clarify how each head contributes to the observed steps, we have constructed heterodimeric kinesins that consist of two distinct heads. The heterodimers in which one of the heads is mutated in a microtubule-binding loop moved processively, even when the parent mutant homodimers bound too weakly to retain microtubules in microtubule-gliding assays. The velocities of the heterodimers were only slightly higher than those of the mutant homodimers, although mixtures of these weak-binding mutant homodimers and the WT dimers moved microtubules at a velocity similar to the WT. Thus, the mutant head affects the motility of the WT head only when they are in the same molecule. The maximum force a single heterodimer produced in optical trapping nanometry was intermediate between the WT and mutant homodimers, indicating that both heads contribute to the maximum force at the same time. These results demonstrate close collaboration of kinesin's two heads in producing force and motility.
Exploiting the virtue of redundancy

Bernstein suggests that redundancy is the main reason for the superb dexterity of human motor control. However, introducing redundancy in an inversely controlled object, results in an ill-posed problem. We suggest learning all the possible solutions and choosing one of them in real time. In this paper we define redundancy and differentiate between finite, countable and uncountable redundancy. We introduce a general concept of multiple controller and describe a specific architecture, the polyhedral mixture of linear experts (PMLE). We extend some notions of learning theory to the case of multiple valued functions and stress the difference between estimated inverse and inverse estimation. Then we show that the multiple inverse PMLE is suitable in serving as a multiple controller.
Aalborg Universitet Low Voltage Ride-Through of Two-Stage Grid-Connected Photovoltaic Systems Through the Inherent Linear Power-Voltage Characteristic

In this paper, a cost-effective control scheme for twostage grid-connected PhotoVoltaic (PV) systems in Low Voltage Ride-Through (LVRT) operation is proposed. In the case of LVRT, the active power injection by PV panels should be limited to prevent from inverter over-current and also energy aggregation at the dc-link, which will challenge the dc-link capacitor lifetime if remains uncontrolled. At the same time, reactive currents should be injected upon any demand imposed by the system operators. In the proposed scheme, the two objectives can be feasibly achieved. The active power is regulated automatically through a proportional controller according to the voltage sag level and PV inherent characteristics (i.e., the voltage and power droop). Compared to prior-art LVRT schemes, the proposed method is cost-effective, as it is achieved by simply plugging the proportional controller into a maximum power point tracking controller without significant hardware or software modifications. In this way, the PV system will not operate at the maximum power point, whereas the inverter will not face any over-current challenge but can provide reactive power support in response to the grid voltage fault. Simulations have been performed on a 3kW two-stage grid-connected single-phase PV system in the case of LVRT operation, where the results have verified the proposed control scheme in terms of fast dynamics and seamless operation mode transitions.
Cost-effectiveness of Negative Pressure Wound Therapy for Postsurgical Patients in Long-term Acute Care

OBJECTIVES: To evaluate the cost-effectiveness of negative pressure wound therapy (NPWT) using reticulated open-cell foam (NPWT/ROCF) as delivered by a Vacuum-Assisted Closure* (KCI Licensing, Inc, San Antonio, Texas) in patients with complex wounds in a long-term acute care (LTAC) setting. These patients are routinely discharged to LTAC hospitals with the goal of accelerating wound healing and timely transfer to a lower acuity care setting and are usually affected with serious comorbidities and deep, complex wounds with exposed anatomical structures, which require extended care (stay > 25 days). DESIGN: A retrospective chart review was conducted to determine the average daily wound volume reduction, average daily wound area reduction, and average cost per cubic centimeter of wound volume reduction for patients treated with NPWT/ROCF as compared with topical advanced moist healing strategies (non-NPWT). SETTING: All patients received treatment in an LTAC hospital. PARTICIPANTS: Patients admitted from November 2001 to August 2004 were identified using a computerized hospital database. The inclusion criteria were postsurgical patients of at least 18 years of age, with a single acute wound. INTERVENTION: Patients were treated with either NPWT/ROCF or advanced moist wound-healing therapies (non-NPWTs). MEASUREMENTS: Data collected included age, sex, wound measurements, Bates-Jensen Wound Assessment Tool severity score, procedures performed, wound care products and devices used, wound-healing outcomes, and costs associated with treatment. RESULTS: Fifty-one patients met the inclusion criteria: 36 were identified as NPWT/ROCF and 15 as non-NPWT. The NPWT/ROCF patients showed a statistically significantly higher average daily rate of volume reduction as compared with the advanced moist wound-healing group (5.02 ± 13.36 vs 0.40 ± 0.88 cm3/day; P = .046). The cost per cubic centimeter reduction was $11.90/cm3 in the NPWT/ROCF group versus $30.92/cm3 in the moist wound-healing group. CONCLUSION: Postsurgical LTAC patients who were treated by NPWT/ROCF had a more accelerated rate of wound closure, compared with patients treated with advanced moist wound-healing therapy. These results suggest that, for this patient group, NPWT/ROCF may be more clinically effective in reducing wound volume, compared with advanced moist wound healing. Furthermore, the lower cost per cubic centimeter volume reduction suggests that NPWT/ROCF produces a more favorable cost-effective solution. Therefore, it is important when developing a wound-healing strategy that cost decisions be based on overall cost and not individual product cost when using advanced technology as part of the overall treatment plan. This study serves as a basis for further work in cost-benefit analysis when considering evidence-based outcomes in wound care.
Molecular Characterization of New Natural Hybrids of Saccharomyces cerevisiae and S. kudriavzevii in Brewing

ABSTRACT We analyzed 24 beer strains from different origins by using PCR-restriction fragment length polymorphism analysis of different gene regions, and six new Saccharomyces cerevisiae × Saccharomyces kudriavzevii hybrid strains were found. This is the first time that the presence in brewing of this new type of hybrid has been demonstrated. From the comparative molecular analysis of these natural hybrids with respect to those described in wines, it can be concluded that these originated from at least two hybridization events and that some brewing hybrids share a common origin with wine hybrids. Finally, a reduction of the S. kudriavzevii fraction of the hybrid genomes was observed, but this reduction was found to vary among hybrids regardless of the source of isolation. The fact that 25% of the strains analyzed were discovered to be S. cerevisiae × S. kudriavzevii hybrids suggests that an important fraction of brewing strains classified as S. cerevisiae may correspond to hybrids, contributing to the complexity of Saccharomyces diversity in brewing environments. The present study raises new questions about the prevalence of these new hybrids in brewing as well as their contribution to the properties of the final product.
Carotid Artery Disease and the Risk of Ischaemic Stroke and Coronary Vascular Events

Information on the presence and extent of carotid arterial wall disease has significant prognostic value. Carotid artery stiffness, intima-media thickness, and early plaque formation are potentially useful predictors of the risk of both ischaemic stroke and coronary heart disease in asymptomatic populations. Early carotid arterial wall disease is also a useful predictor of coronary artery disease on angiography and subsequent coronary vascular events in populations at risk of coronary heart disease. More advanced carotid wall disease (carotid stenosis and plaque surface morphology) is predictive of both ischaemic stroke and coronary heart disease in high-risk populations with established cerebrovascular disease. Plaque characteristics on ultrasound, such as echolucency, may also have a prognostic value. However, in order to identify individuals with high risks of vascular events, this information must be combined with other clinical, laboratory, and imaging data. Ideally, large prospective cohort studies are required in which all these data are recorded and then combined using multivariate statistical modelling. Future studies should also determine the relationship between the various measures of carotid wall disease and the risk of stroke for the different subtypes of ischaemic stroke.
Interpolation in a pixellated CZT γ-radiation detector

We describe a method of interpolation for a pixellated γ-radiation detector made of cadmium zinc telluride (CZT) with the goal to optimize its intrinsic spatial resolution. A similar method is known from silicon strip sensors where the interpolation improves the intrinsic spatial resolution over the single-strip digital resolution.
Integrated kinetics of X chromosome inactivation in differentiating embryonic stem cells

Inactivation of the X chromosome during early female development and the subsequent maintenance of this transcriptionally inert state through countless cell divisions remain a paradigm for epigenetic regulation in mammals. Nevertheless, the exact mechanisms underlying this chromosome-wide silencing process remain unclear. Using differentiating female embryonic stem (ES) cells as a model system, we recently found that histone H3 tail modifications are among the earliest known chromatin changes in the X inactivation process, appearing as soon as Xist RNA accumulates on the X chromosome, but prior to transcriptional silencing of X-linked genes (Heard et al., 2001). In this report we present an integrated analysis of the sequence of early events and chromatin modifications underlying X inactivation in differentiating female ES cells. We have extended our previous analysis concerning changes in histone tail modification states. We find that the hypomethylation of Arg-17 and that of Lys-36 on histone H3 also characterize the inactive X chromosome, and that these profiles show a similarly early onset during the initiation of X inactivation. In addition, we have investigated the kinetics of the shift in replication timing of the X chromosome undergoing inactivation. This event occurs slightly later than Xist RNA coating and the chromatin modifications. Finally, from an early stage in the X inactivation process, characteristic histone modification patterns can be found on the X chromosome at mitosis, suggesting that they represent true epigenetic marks of the inactive state.
Empirical performance upper bounds for image and video captioning

The task of associating images and videos with a natural language description has attracted a great amount of attention recently. Rapid progress has been made in terms of both developing novel algorithms and releasing new datasets. Indeed, the state-of-the-art results on some of the standard datasets have been pushed into the regime where it has become more and more difficult to make significant improvements. Instead of proposing new models, this work investigates the possibility of empirically establishing performance upper bounds on various visual captioning datasets without extra data labelling effort or human evaluation. In particular, it is assumed that visual captioning is decomposed into two steps: from visual inputs to visual concepts, and from visual concepts to natural language descriptions. One would be able to obtain an upper bound when assuming the first step is perfect and only requiring training a conditional language model for the second step. We demonstrate the construction of such bounds on MS-COCO, YouTube2Text and LSMDC (a combination of M-VAD and MPII-MD). Surprisingly, despite of the imperfect process we used for visual concept extraction in the first step and the simplicity of the language model for the second step, we show that current state-of-the-art models fall short when being compared with the learned upper bounds. Furthermore, with such a bound, we quantify several important factors concerning image and video captioning: the number of visual concepts captured by different models, the trade-off between the amount of visual elements captured and their accuracy, and the intrinsic difficulty and blessing of different datasets.
Decreased expression of calcium-sensing receptor messenger ribonucleic acids in parathyroid adenomas.

BACKGROUND The set point for parathyroid hormone (PTH) secretion is increased in patients with primary hyperparathyroidism, possibly because of receptor defect(s). A decreased expression of calcium receptor (CaR) messenger ribonucleic acid (mRNA) and protein and a decreased expression of the putative calcium-sensing CAS (gp330/megalin) protein have been demonstrated in parathyroid adenomas. METHODS Expression of CAS mRNA was studied in matched pairs of adenomas and adenoma-associated biopsy specimens from normal parathyroid glands from 15 patients with sporadic primary hyperparathyroidism. Cryostat sections were hybridized with an oligonucleotide complementary to CAS mRNA, rinsed, air dried, and exposed to x-ray film for semiquantification of radioactivity. RESULTS Expression of CAS mRNA in the adenomas was lowered significantly to 25% (median; range 9% to 80%) of that of the corresponding biopsy specimens of normal parathyroid glands. No correlation was seen between CAS mRNA in the adenoma and preoperative serum calcium levels, PTH level, or weight of the adenoma. The levels of CAS mRNA were significantly lower than those observed previously for CaR mRNA. There was no significant correlation between the levels of CAS and CaR mRNA. CONCLUSIONS Lowered levels of receptors sensing extracellular calcium (CaR and CAS) probably contribute to the increased set point for PTH secretion in primary hyperparathyroidism.
The Role of Cyclooxygenase and Lipoxygenase in Cancer Chemoprevention

The involvement of prostaglandins (PGs) and other eicosanoids in the development of human cancer has been known for over two decades. Importantly, an increase in PG synthesis may influence tumor growth in human beings and experimental animals, and numerous studies have illustrated the effect of PG synthesis on carcinogen metabolism, tumor cell proliferation and metastatic potential. PGs produced by cyclooxygenases (COXs) are represented by a large series of compounds that mainly enhance cancer development and progression, acting as carcinogens or tumor promoters, with profound effects on carcinogenesis. Further investigations suggest that arachidonic acid (AA) metabolites derived from lipoxygenase (LOX) pathways play an important role in growth-related signal transduction, implying that intervention through these pathways should be useful for arresting cancer progression. We discuss here the implications of COX and LOX in colon, pancreatic, breast, prostate, lung, skin, urinary bladder and liver cancers. Select inhibitors of COX and LOX are described, including nonsteroidal antiinflammatory drugs (NSAIDs), selective COX-2 inhibitors, curcumin, tea, silymarin and resveratrol, as well as a method useful for evaluating inhibitors of COX. Although a substantial amount of additional work is required to yield a better understanding of the role of COX and LOX in cancer chemoprevention, it is clear that beneficial therapeutic effects can be realized through drug-mediated modulation of these metabolic pathways.
High infectious risk donors: what are the risks and when are they too high?

Purpose of reviewHigh infectious risk donors (HRDs) fall into a behavioral category thought to increase risk of infectious transmission through transplantation; despite controversy surrounding their use, they comprise almost 9% of donors in which at least one organ is recovered. This review seeks to describe national patterns in utilization, attitudes toward HRDs, and strategies to minimize and quantify infectious risks. Recent findingsHRD organs are discarded at a higher rate than non-HRDs, and many surgeons have decreased the use of HRDs in response to a recent widely publicized case of HIV and hepatitis C virus (HCV) transmission. Special informed consent use can mitigate legal risk and might increase provider comfort with HRD utilization. Nucleic acid testing (NAT) mitigates infectious risk by decreasing the window period, particularly for HCV in which the risk of undetected window period infection decreases by an order of magnitude. Estimated risk of undetected window period HIV infection varies by HRD behavior category (range 0.035–4.9 per 10 000 donors when NAT is used), HCV risk is higher (range 0.027–32.4 per 10 000). SummaryGiven long waiting times and high waitlist mortality, organs from HRDs can be used to expand the organ supply. Estimates of HRD infectious risk can be used to guide patient and provider decision making.
A spatiotemporal indexing approach for efficient processing of big array-based climate data with MapReduce

ABSTRACT Climate observations and model simulations are producing vast amounts of array-based spatiotemporal data. Efficient processing of these data is essential for assessing global challenges such as climate change, natural disasters, and diseases. This is challenging not only because of the large data volume, but also because of the intrinsic high-dimensional nature of geoscience data. To tackle this challenge, we propose a spatiotemporal indexing approach to efficiently manage and process big climate data with MapReduce in a highly scalable environment. Using this approach, big climate data are directly stored in a Hadoop Distributed File System in its original, native file format. A spatiotemporal index is built to bridge the logical array-based data model and the physical data layout, which enables fast data retrieval when performing spatiotemporal queries. Based on the index, a data-partitioning algorithm is applied to enable MapReduce to achieve high data locality, as well as balancing the workload. The proposed indexing approach is evaluated using the National Aeronautics and Space Administration (NASA) Modern-Era Retrospective Analysis for Research and Applications (MERRA) climate reanalysis dataset. The experimental results show that the index can significantly accelerate querying and processing (~10× speedup compared to the baseline test using the same computing cluster), while keeping the index-to-data ratio small (0.0328%). The applicability of the indexing approach is demonstrated by a climate anomaly detection deployed on a NASA Hadoop cluster. This approach is also able to support efficient processing of general array-based spatiotemporal data in various geoscience domains without special configuration on a Hadoop cluster.
Treatment of Inoperable Coronary Disease and Refractory Angina: Spinal Stimulators, Epidurals, Gene Therapy, Transmyocardial Laser, and Counterpulsation

Intractable angina from refractory coronary disease is a severe form of myocardial ischemia for which revascularization provides no prognostic benefit. Inoperable coronary disease is also accompanied by a “vicious cycle” of myocardial dystrophy from a chronic alteration of the cardiac sympathetic tone and sensitization of damaged cardiac tissues. Several adjunctive treatments have demonstrated efficacy when revascularization is either unsuccessful or contraindicated. Spinal cord stimulation modifies the neurologic input and output of the heart by delivering a very low dose of electrical current to the dorsal columns of the high thoracic spinal cord. Neural fibers then release CGRP and other endogenous peptides to the coronary circulation reducing myocardial oxygen demand and enhancing vasodilation of collaterals to improve the myocardial blood flow of the most diseased regions of the heart. Randomized study has shown the survival data at five years is comparable to bypass for high-risk patients. Transmyocardial laser revascularization creates small channels into ischemic myocardium in an effort to enhance flow though studies have shown no improvement in prognosis over medical therapy alone. Enhanced external counterpulsation uses noninvasive pneumatic compression of the legs to improve diastolic filling of the coronary vessels and promote development of collateral flow. The compressor regimen requires thirty-five hours of therapy over a seven-week treatment period. Therapeutic angiogenesis requires injection of cytokines to promote neovascularization and improve myocardial perfusion into the regions affected by chronic ischemia. Phase 3 trials are pending. High thoracic epidural blockade produces a rapid and potent sympatholysis, coronary vasodilation and reduced myocardial oxygen demand in refractory coronary disease. This technique can be used as an adjunct to bypass surgery or medical therapy in chronic or acute unstable angina. Epidurals are easy to perform and often available for outpatient or inpatient use. The rapid anti-ischemic effect may complement therapeutic angiogenesis or other interventions with delayed onset to clinical benefit. A new era for interventional and implant cardiology is beginning to emerge as more clinicians, including cardiologists, gradually learn new procedures to safely provide more therapeutic options for patients suffering refractory angina.
A high density COX1 barcode oligonucleotide array for identification and detection of species of Penicillium subgenus Penicillium

We developed a COX1 barcode oligonucleotide array based on 358 sequences, including 58 known and two new species of Penicillium subgenus Penicillium, and 12 allied species. The array was robotically spotted at near microarray density on membranes. Species and clade‐specific oligonucleotides were selected using the computer programs SigOli and Array Designer. Robotic spotting allowed 768 spots with duplicate sets of perfect match and the corresponding mismatch and positive control oligonucleotides, to be printed on 2 × 6 cm2 nylon membranes. The array was validated with hybridizations between the array and digoxigenin (DIG)‐labelled COX1 polymerase chain reaction amplicons from 70 pure DNA samples, and directly from environmental samples (cheese and plants) without culturing. DNA hybridization conditions were optimized, but undesired cross‐reactions were detected frequently, reflecting the relatively high sequence similarity of the COX1 gene among Penicillium species. Approximately 60% of the perfect match oligonucleotides were rejected because of low specificity and 76 delivered useful group‐specific or species‐specific reactions and could be used for detecting certain species of Penicillium in environmental samples. In practice, the presence of weak signals on arrays exposed to amplicons from environmental samples, which could have represented weak detections or weak cross reactions, made interpretation difficult for over half of the oligonucleotides. DNA regions with very few single nucleotide polymorphisms or lacking insertions/deletions among closely related species are not ideal for oligonucleotide‐based diagnostics, and supplementing the COX1‐based array with oligonucleotides derived from additional genes would result in a more robust hierarchical identification system.