Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular investigation of a dicentric 13;17 chromosome found in a 21-week gestation fetus with multiple congenital abnormalities

We report a 21-week gestation fetus terminated because of multiple congenital abnormalities seen on ultrasound scan, including ventriculomegaly, possible clefting of the hard palate, cervical hemivertebrae, micrognathia, abnormal heart, horseshoe kidney and a 2-vessel umbilical cord. On cytogenetic examination, the fetus was found to have a male karyotype with 45 chromosomes with a dicentric chromosome, which appeared to consist of the long arms of chromosomes 13 and 17. Molecular genetic investigations and fluorescence in situ hybridization (FISH) unexpectedly showed that the derivative chromosome contained two interstitial blocks of chromosome 17 short arm sequences, totalling approximately 7 Mb, between the two centromeres. This effectively made the fetus monosomic for ∼15 Mb of 17p without the concurrent trisomy for another chromosome normally seen following malsegregation of reciprocal translocations. It also illustrates the complexity involved in the formation of some structurally abnormal chromosomes, which can only be resolved by detailed molecular investigations.
Deployment of a Multi-site Cloud Environment for Molecular Virtual Screenings

With the constant increase in the number and variety of small molecule chemical compounds, drug discovery is becoming a very resource intensive endeavor. Performing molecular simulations of ligand-protein binding by virtual screening has become an integral part of the discovery process. Cloud computing is an efficient choice to execute these large-scale screenings, given that large compute allocations are not accessible to many researchers. This research focused on developing a multi-site cloud environment that combines small allocations of virtual machines in multiple locations connected through a virtual networking system (ViNe), and compared two parallelization approaches: Message Passing Interface (MPI) and MapReduce using Hadoop. Virtual screenings were conducted using DOCK, a protein-ligand molecular interaction simulation program. Multiple DOCK test simulations through MPI and Hadoop were run to assess the performance and flexibility of the environment. These tests indicated that MPI and MapReduce offer comparable scalability performance, and that network latency has a significant influence on low accuracy simulations. Furthermore, differences in performance at individual cloud resource sites were reduced on average because of the larger combined pool of resources. This project prototyped and assessed a fully functional multi-site cloud environment for virtual screenings, which can be used to guide small laboratories in deploying their own cloud-based screenings.
Prospective comparison of 18F-FDG PET with conventional imaging modalities (MRI, CT, and 67Ga scintigraphy) in assessment of combined intraarterial chemotherapy and radiotherapy for head and neck carcinoma.

UNLABELLED To preserve the oral organs and functions in patients with head and neck carcinoma, accurate determination of the appropriate treatment after neoadjuvant chemotherapy and radiotherapy is of critical importance. We evaluated the diagnostic accuracy of (18)F-FDG PET relative to that of other conventional imaging modalities in the assessment of therapeutic response after combined intraarterial chemotherapy and radiotherapy as an organ preservation protocol. METHODS The study was prospectively performed on 23 consecutive patients with head and neck squamous cell carcinoma who completed the treatment regimen and underwent 2 (18)F-FDG PET studies before and after neoadjuvant chemoradiotherapy. (67)Ga scintigraphy (only before therapy) as well as MRI and CT (both before and after therapy) were also performed. All images were blindly and independently interpreted without knowledge of histologic findings. The level of confidence in image interpretation was graded by means of a 5-point rating system (0 = definitely no tumor to 4 = definite tumor). RESULTS Before treatment, (18)F-FDG PET detected primary tumors in all 23 patients and was more sensitive (100%) than MRI (18/23; 78.3%), CT (15/22; 68.2%), and (67)Ga scintigraphy (8/20; 40%), with a confidence level of 3 or 4 as a positive tumor finding. After chemoradiotherapy, residual tumors were histologically confirmed in 4 patients (pathologic complete response rate, 19/23; 82.6%). Although posttreatment (18)F-FDG PET showed almost equal sensitivity (4/4; 100%) compared with MRI (3/3; 100%) or CT (3/4; 75%), its specificity (17/19; 89.5%) was superior to MRI (7/17, 41.2%) and to CT (10/17; 58.8%) for primary lesions. Regarding metastases to neck lymph nodes, only specificity for posttreatment images was calculated because no metastasis was confirmed in any patients after treatment. Six subjects had (18)F-FDG PET-positive lymph nodes, which had pathologically no tumor cells and suggested an inflammatory reactive change after therapy. Therefore, the specificity of posttreatment (18)F-FDG PET (17/23; 73.9%) was almost identical to that of MRI (17/20; 85%) and CT (16/21; 76.2%) for neck metastasis. With combined chemoradiotherapy monitored with (18)F-FDG PET, 8 patients avoided surgery and the remaining 15 patients underwent a reduced form of surgery. CONCLUSION (18)F-FDG PET facilitates differentiation of residual tumors from treatment-related changes after chemoradiotherapy, which may be occasionally difficult to characterize by anatomic images. (18)F-FDG PET has a clinical impact for the management of patients with head and neck cancers after neoadjuvant chemoradiotherapy by optimizing surgical treatment for each patient and contributes to the improvement of the patient's quality of life.
Resource scheduling based on cooperative particle swarm optimization in trusted computing environment

In trust-based network computing environment, in order to establish a harmonious network environment, and enhance the network resources sharing utilization, resources scheduling research faces more problems than ever before. A resource scheduling algorithm, using cooperative particle optimization and putting task completion price and overall system trust benefits as optimized object, is proposed based on the trust model proposed by Internet-based Virtual Computing Environment (iVCE). Simulation results indicate that the algorithm has obvious performance advantage in the aspects of whole system credibility and resource utilization rate than other classic scheduling algorithms. The algorithm can realize rational scheduling of network resources, and optimize the system performance in trusted computing environment.
Neurodevelopmental Outcomes in Children with Down Syndrome and Infantile Spasms

Abstract Down syndrome (DS) is the most common genetic cause of intellectual disability in the United States. The prevalence of seizure in individuals with DS is 1 to 13%, and infantile spasm (IS) occurs in 6 to 32% of those with seizures. Since IS is relatively common in children with DS, it is important to understand the impact IS has on the neurodevelopmental outcomes to provide appropriate anticipatory guidance to help maximize the potential of these children. Our study is the first to compare the neurodevelopmental outcomes of children with DS and IS (DS + IS) to children with DS and no history of seizures (DS − IS). Using the Bayley scales of infant and Toddler development III, we assessed the neurodevelopment of 29 subjects (8 DS + IS and 21 DS − IS). Neurodevelopmental outcome was poor in the DS + IS cohort, but the delay in treatment does not appear to contribute to any differences in their developmental scores. However, when compared with children with DS − IS, the DS + IS cohort scored approximately 20 points less in all domains including cognitive, motor, and language (p < 0.05). Our results indicate that IS may impact the neurodevelopmental outcomes of children with DS + IS; thus, it is important to provide ongoing developmental and educational assessments and potentially additional therapies for children with DS + IS.
High-Order Vector Control of Grid-Connected Voltage-Source Converters With LCL-Filters

This paper proposes a vector control strategy for LCL-filter-based grid-connected voltage-source converters (VSCs). The proposed control strategy is inherently capable of attenuating the resonance phenomenon of such systems. This is an advantage over the existing methods, which require additional damping techniques. Moreover, the proposed vector control strategy is able to fully decouple the direct (d) and quadrature (q) components of the current in a rotating reference frame. The design procedure comprises a constrained optimization-based loop shaping. It utilizes the multi-input multi-output (MIMO) nonparametric model of the system along with a high-order linearly parameterized MIMO controller to form an open-loop transfer function matrix. Minimizing the second norm of the error between the open-loop transfer function matrix and a desired one, the coefficients of the controller are optimally determined. Conducting several reference tracking scenarios, the performance of the proposed vector controller is evaluated both by means of time-domain simulation studies in MATLAB/Simulink and experimental results.
Truncated Sequential Spectrum Sensing for Cognitive Radio Networks

Reliable spectrum sensing is a key functionality of a cognit ive radio network. Cooperative spectrum sensing improves the detection reliability of a cognitive r adio system but also increases the system energy consumption which is a critical factor particularly for low -power wireless technologies. A censored truncated sequential spectrum sensing technique is consid ered as an energy-saving approach. To design the underlying sensing parameters, the maximum average ene rgy consumption per sensor is minimized subject to a lower bounded global probability of detection a nd n upper bounded false alarm rate. This way both the interference to the primary user due to miss dete ction and the network throughput as a result of a low false alarm rate are controlled. To solve this proble m, it is assumed that the cognitive radios and fusion center are aware of their location and mutual channel properties. We compare the performance of the proposed scheme with a fixed sample size censoring sche me under different scenarios and show that for low-power cognitive radios, censored truncated se quential sensing outperforms censoring. It is shown that as the sensing energy per sample of the cognitive r adios increases, the energy efficiency of the censored truncated sequential approach grows significa ntly.
Comparison of UV-Induced Inactivation and RNA Damage in MS2 Phage across the Germicidal UV Spectrum

ABSTRACT Polychromatic UV irradiation is a common method of pathogen inactivation in the water treatment industry. To improve its disinfection efficacy, more information on the mechanisms of UV inactivation on microorganisms at wavelengths throughout the germicidal UV spectrum, particularly at below 240 nm, is necessary. This work examined UV inactivation of bacteriophage MS2, a common surrogate for enteric pathogens, as a function of wavelength. The bacteriophage was exposed to monochromatic UV irradiation from a tunable laser at wavelengths of between 210 nm and 290 nm. To evaluate the mechanisms of UV inactivation throughout this wavelength range, RT-qPCR (reverse transcription-quantitative PCR) was performed to measure genomic damage for comparison with genomic damage at 253.7 nm. The results indicate that the rates of RNA damage closely mirror the loss of viral infectivity across the germicidal UV spectrum. This demonstrates that genomic damage is the dominant cause of MS2 inactivation from exposure to germicidal UV irradiation. These findings contrast those for adenovirus, for which MS2 is used as a viral surrogate for validating polychromatic UV reactors.
CCB 2005: Towards developing a monitoring framework for Multiple Species Habitat Conservation Plans. Part I.

UNIVERSITY OF CALIFORNIA, RIVERSIDE BERKELEY DAVIS IRVINE LOS ANGELES MERCED RIVERSIDE SAN DIEGO SAN FRANCISCO SANTA BARBARA SANTA CRUZ C ENTER FOR C ONSERVATION B IOLOGY R IVERSIDE , C ALIFORNIA 92521-0122 TEL : 951-827-5484; FAX : 951-827-4625 C OLLEGE OF N ATURAL A ND A GRICULTURAL S CIENCES C ITRUS R ESEARCH C ENTER AND A GRICULTURAL E XPERIMENT S TATION CCB 2005: Towards developing a monitoring framework for Multiple Species Habitat Conservation Plans. Part I. Michael F. Allen, Director John Rotenberry, Associate Director Thomas Scott, Associate Director Ken Halama, Project Coordinator Kristine Preston, WRC MSHCP Project Manager Cooperating Faculty Edith Allen Bai-Lian Li Richard Minnich Richard Redak Andrew Sanders Post-Doctoral Research Associates Xiongwen Chen Wendy Hodges Monica Swartz Graduate Students Karen Bagne Cameron Barrows Sharon Coe Robert Cox Jill Deppe Laramy Enders Lori Hargrove Jason Hlebakos Anna Howell Pey-Yi Lee Myong-Bok Li Adam Malisch Senanu Pearson Susanna Peluc Kim Oldehoft Allison Rudaleveige (Pettis) Laurel Salzman Ginny Short Greg Smith Robert Steers Andrew Stoehr Research Staff and Associates Michael Aspell Roxanne Broadway Patricia Brock Jolene Cassano Antonio Celis Kathleen Fleming Darrell Hutchinson Sheila Kee Kristen Larsen Eliza Maher Wendy Mello Brandon Mutrux Orlay Plummer Nanette Pratini Tom Prentice Tim Redman Vanessa Rivera Del Rio Veronique Rorive Marisa Sripracha Tracy Tennant Chris True Undergraduate Students Lonnie Bachor Chris Glover Daniel Guy Amber Holt Emma Middlemiss Melissa Mutrux Melissa Preston Trinity Ryan Nhi Huong Vu Alexander Yun
Maximum Likelihood CT reconstruction from material-decomposed sinograms using fisher information

Recently, a K-edge imaging technique for energy-resolving photon-counting detectors based on Maximum-Likelihood estimation for material separation in the projection domain with subsequent image formation using filtered back projection (FBP) was presented. Despite its computational load, use of statistical reconstruction techniques for image reconstruction from material-specific sinograms is favourable as they feature superior signal to noise ratio (SNR). This work presents an estimation of the noise in material-decomposed sinograms using Fisher information in order to enable statistical image reconstruction. Simulations demonstrate that a gain of two in SNR compared to FBP reconstruction can be obtained. This improvement may be used for x-ray dose reduction but is in particular desirable to limit count rates and, thus, which is a significant challenge with current photon-counting detectors.
Heparan sulfate proteoglycan-dependent induction of axon branching and axon misrouting by the Kallmann syndrome gene kal-1

Kallmann syndrome is a neurological disorder characterized by various behavioral and neuroanatomical defects. The X-linked form of this disease is caused by mutations in the KAL-1 gene, which codes for a secreted molecule that is expressed in restricted regions of the brain. Its molecular mechanism of action has thus far remained largely elusive. We show here that expression of the Caenorhabditis elegans homolog of KAL-1 in selected sensory and interneuron classes causes a highly penetrant, dosage-dependent, and cell autonomous axon-branching phenotype. In a different cellular context, heterologous C. elegans kal-1 expression causes a highly penetrant axon-misrouting phenotype. The axon-branching and -misrouting activities require different domains of the KAL-1 protein. In a genetic modifier screen we isolated several loci that either suppress or enhance the kal-1-induced axonal defects, one of which codes for an enzyme that modifies specific residues in heparan sulfate proteoglycans, namely heparan-6O-sulfotransferase. We hypothesize that KAL-1 binds by means of a heparan sulfate proteoglycan to its cognate receptor or other extracellular cues to induce axonal branching and axon misrouting.
New and Effective Treatment of Experimentally Induced Venous Thrombosis with Anti-inflammatory rPSGL-Ig

Summary Background P-selectin antagonism decreases thrombosis and inflammation in animal models of venous thrombosis (VT) prophylaxis. This study defines results using a P-selectin receptor antagonist for VT treatment. Methods Eight juvenile baboons underwent 6 h of iliofemoral venous stasis to produce an occlusive VT. Two days later, animals were treated for 14 days with rPSGL-Ig, 4 mg/kg (n3), LMWH (n2) or saline (n3) and treatment continued weekly (rPSGL-Ig) or daily (LMWH, saline). The animals were examined and sacrificed 14 days after treatment initiation (n4) or on day 90 (n4). Results Percent spontaneous vein reopening revealed a significant increase (p <0.05) in the proximal iliac vein in rPSGL-Ig and LMWH animals compared to controls (62%, 70% vs 8%), without differences in inflammation. No anticoagulation, thrombocytopenia, or wound complications were found in rPSGL-Ig animals. At 90 days, recanalization with iliac vein valve competence was found in treated animals. Conclusion rPSGLIg successfully treated established VT without anticoagulation.
Variation in motor threshold with frequency using kHz frequency alternating current

We investigated the frequency dependence of motor thresholds over the frequency range 1 kHz to 25 kHz. Alternating current (AC), ramped in intensity, was applied transcutaneously, and the induced wrist extensor torque was measured. Plots of log torque versus stimulus voltage were used to accurately determine thresholds. Three kinds of sinusoidal AC stimuli were compared: continuous, 10 ms bursts at 50 Hz, and 50‐Hz single‐cycle. Differences were attributed to summation of subthreshold depolarizations. The variation in relative thresholds (continuous/single‐cycle and burst/single‐cycle) indicates that summation occurs more efficiently at higher kHz frequencies. The observed frequency and waveform dependence provides evidence for high‐frequency nerve fiber firing rates and fiber dropout when continuous or modulated AC is used, with the effects increasing with AC frequency. The form of the motor response evoked at high frequencies has features that suggest that frequencies above 10‐kHz have little or no useful clinical role in rehabilitation procedures. © 2001 John Wiley & Sons, Inc. Muscle Nerve 24: 1303–1311, 2001
Optimal PMU placement for topological observability of power system: Robust measurement design in the space of phasor variables

This paper presents a new mixed-integer linear programming formulation of the optimal phasor measurement units (PMUs) placement problem when considering the topological observability of the power system. Different from other formulations, decision variables are associated with phasor measurements, but not with PMUs. This approach makes it easy to take into account the availability of PMU measuring channels, effect of zero-injection bus, possible system contingencies like single PMU or branch loss, as well as gross error occurrence, and offers flexibility in specifying the objective function. Paper describes a presolve technique that makes the formulation more compact and tighter. Numerical results on IEEE standard test systems are presented and reveal the existence of the PMU placements which ensure topological observability, but fail to meet numerical observability.
A Knowledge Management Framework for Knowledge-Intensive SMEs

Nowadays knowledge-intensive enterprises, which offer knowledge-based products and services to the market, play a vital role in the knowledge-based economy. Effective knowledge management has become a key success factor for those enterprises in particular and the whole economy in general. Knowledge management is important for both large and small and medium knowledge-intensive enterprises; however, there is still a little focus on this topic in knowledge-intensive small and medium enterprises (SMEs). In this study, the authors propose an integrated framework as a foundation for designing an appropriate knowledge management solution for knowledge-intensive SMEs. The paper begins with a theoretical background and the research design and then continues with the characteristics of the framework. Accordingly, the principal components of the framework corresponding to design science research such as the constructs, model, method and instantiations are illustrated. The paper ends with the conclusions and future work.
Structure‐based discovery of novel US28 small molecule ligands with different modes of action

The human cytomegalovirus‐encoded G protein‐coupled receptor US28 is a constitutively active receptor, which can recognize various chemokines. Despite the recent determination of its 2.9 Å crystal structure, potent and US28‐specific tool compounds are still scarce. Here, we used structural information from a refined US28:VUF2274 complex for virtual screening of >12 million commercially available small molecule compounds. Using a combined receptor‐ and ligand‐based approach, we tested 98 of the top 0.1% ranked compounds, revealing novel chemotypes as compared to the ~1.45 million known ligands in the ChEMBL database. Two compounds were confirmed as agonist and inverse agonist, respectively, in both IP accumulation and Ca2+ mobilization assays. The screening setup presented in this work is computationally inexpensive and therefore particularly useful in an academic setting as it enables simultaneous testing in binding as well as in different functional assays and/or species without actual chemical synthesis.
Purification and characterization of extracellular laccase produced by Ceriporiopsis subvermispora and decolorization of triphenylmethane dyes

Laccases of white‐rot fungi provide a promising future as a tool to be used in the field of biodegradation of synthetic dyes with different chemical structures. The aim of this study was production, characterization, and application of laccases from the white‐rot fungus Ceriporiopsis subvermispora ATCC 90467 for decolorization of triphenylmethane dyes that could remain persistent in wastewater. Laccase was purified from a C. subvermispora culture by a four‐step method resulting high specific activity of 2,571 U g−1, 88‐fold higher than crude laccase. Purified laccase (molecular weight 45 kDa) had the optimum activity at pH 2.0 and the optimum temperature 50 °C using ABTS as chromogenic substrate. Laccases efficiently decolorized triphenylmethane dyes such as Malachite Green (87.8%), Bromocresol Purple (71.6%), and Methyl Violet (68.1%) without redox mediator. However, decolorization percentage of hardly degradable triphenylmethane dyes such as Phenol Red, Bromophenol Blue, and Brilliant Blue R‐250 was increased the presence of some low‐molecular weight compounds (natural or synthetic redox mediators). Purified laccases were resistant to Mg2+, Ca2+, Ba2+, Mn2+, Fe2+, Cu2+, Zn2+, and Sn2+ (10 mmol L−1). These findings suggest that laccases from C. subvermispora are able to decolorize triphenylmethane dyes without the negative influence of metal ions that can be found in wastewater.
New Bidirectional ZVS PWM Sepic/Zeta DC-DC Converter

Bidirectional DC-DC converters allow transfer of power between two dc sources, in either direction. Due to their ability to reverse the direction of flow of power, they are being increasingly used in many applications such as battery charger/dischargers, dc uninterruptible power supplies, electrical vehicle motor drives, aerospace power systems, telecom power supplies, etc. This paper proposes a new bidirectional Sepic/Zeta converter. It has low switching loss and low conduction loss due to auxiliary communicated circuit and synchronous rectifier operation, respectively. Because of positive and buck/boost-like DC voltage transfer function (M=D/1-D), the proposed converter is desirable for use in distributed power system. The proposed converter also has both transformer-less version and transformer one.