gebhart/patrepeval huggingface dataset:
Preliminary assessment of dispersion versus absorption analysis of high spectral and spatial resolution magnetic resonance images in the diagnosis of breast cancer (2015)

Water resonance lineshapes observed in breast lesions imaged with high spectral and spatial resolution (HiSS) magnetic resonance imaging have been shown to contain diagnostically useful non-Lorentzian components. The purpose of this work is to update a previous method of breast lesion diagnosis by including phase-corrected absorption and dispersion spectra. This update includes information about the shape of the complex water resonance, which could improve the performance of a computer-aided diagnosis breast lesion classification scheme. The non-Lorentzian characteristics observed in complex breast lesion water resonance spectra are characterized by comparing a plot of the real versus imaginary components of the spectrum to that of a perfect complex Lorentzian spectrum, a "dispersion versus absorption" (DISPA) analysis technique. Distortion in the shape of the observed spectra indicates underlying physiologic changes, which have been shown to be correlated with malignancy. These spectral shape distortions in each lesion voxel are quantified by summing the deviations in DISPA radius from an ideal complex Lorentzian spectrum over all Fourier components, yielding a "total radial difference" (TRD). We limited our analysis to those voxels in each lesion with the largest TRD. The number of voxels considered was dependent on the lesion size. The TRD was used to classify voxels from 15 malignant and 8 benign lesions ([Formula: see text] voxels after voxel elimination). Lesion discrimination performance was evaluated for both the average and variance of the TRD within each lesion. Area under the receiver operating characteristic curve (ROC AUC) was used to assess both the voxel- and lesion-based discrimination methods in the task of distinguishing between malignant and benign. In the task of distinguishing voxels from malignant and benign lesions, TRD yielded an AUC of 0.89 (95% confidence interval [0.84, 0.91]). In the task of distinguishing malignant from benign lesions, the average radial difference yielded an AUC of 0.90 (95% confidence interval [0.71, 1.00]) and the variance in the radial difference yielded an AUC of 0.84 (95% confidence interval [0.61, 0.99]). We have applied the DISPA spectroscopic analysis method to HiSS data in order to identify and quantify voxels in breast lesions displaying non-Lorentzian characteristics. We have shown that a breast lesion classification scheme based on the absorption and dispersion spectral data obtained from HiSS acquisitions may outperform a similar classifier based on single off-peak component analysis, as it uses shape details of the entire spectrum instead of the magnitude at a single spectral location.
The Slice Is Served: Enforcing Radio Access Network Slicing in Virtualized 5G Systems (2019)

The notions of softwarization and virtualization of the radio access network (RAN) of next-generation (5G) wireless systems are ushering in a vision where applications and services are physically decoupled from devices and network infrastructure. This crucial aspect will ultimately enable the dynamic deployment of heterogeneous services by different network operators over the same physical infrastructure. RAN slicing is a form of 5G virtualization that allows network infrastructure owners to dynamically "slice" and "serve" their network resources (i.e., spectrum, power, antennas, among others) to different mobile virtual network operators (MVNOs), according to their current needs. Once the slicing policy (i.e., the percentage of resources assigned to each MVNO) has been computed, a major challenge is how to allocate spectrum resources to MVNOs in such a way that (i) the slicing policy defined by the network owner is enforced; and (ii) the interference among different MVNOs is minimized. In this article, we mathematically formalize the RAN slicing enforcement problem (RSEP) and demonstrate its NP-hardness. For this reason, we design three approximation algorithms that render the solution scalable as the RSEP increases in size. We extensively evaluate their performance through simulations and experiments on a testbed made up of 8 software-defined radio peripherals. Experimental results reveal that not only do our algorithms enforce the slicing policies, but can also double the total network throughput when intra-MVNO power control policies are used in conjunction.
High‐Throughput Fabrication of Uniform and Homogenous MOF Coatings (2011)

Abstract We describe a novel method to produce monolithic, oriented, crystalline and highly porous coatings on solid substrates. By adopting the recently described liquid‐phase epitaxy (LPE) process developed to grow metal‐organic framework coatings (MOFs) on modified Au‐substrates to the spray method, we have prepared thick (μm) layers of several MOF types on modified Au‐substrates, including HKUST‐I and layer‐pillar MOFs. The spray method not only allows such SURMOFs to be grown much faster than with the LPE‐process but the dependence of layer thickness on the number of immersion cycles also provides valuable insights into the mechanism governing the layer‐by‐layer MOF formation process.
Decreased IL7Rα and TdT expression underlie the skewed immunoglobulin repertoire of human B-cell precursors from fetal origin (2016)

Newborns are unable to mount antibody responses towards certain antigens. This has been related to the restricted repertoire of immunoglobulin (Ig) genes of their B cells. The mechanisms underlying the restricted fetal Ig gene repertoire are currently unresolved. We here addressed this with detailed molecular and cellular analysis of human precursor-B cells from fetal liver, fetal bone marrow (BM), and pediatric BM. In the absence of selection processes, fetal B-cell progenitors more frequently used proximal V, D and J genes in complete IGH gene rearrangements, despite normal Ig locus contraction. Fewer N-nucleotides were added in IGH gene rearrangements in the context of low TdT and XRCC4 expression. Moreover, fetal progenitor-B cells expressed lower levels of IL7Rα than their pediatric counterparts. Analysis of progenitor-B cells from IL7Rα-deficient patients revealed that TdT expression and N-nucleotides additions in Dh-Jh junctions were dependent on functional IL7Rα. Thus, IL7Rα affects TdT expression, and decreased expression of this receptor underlies at least in part the skewed Ig repertoire formation in fetal B-cell precursors. These new insights provide a better understanding of the formation of adaptive immunity in the developing fetus.
Gradient band gap engineered alloyed quaternary/ternary CdZnSeS/ZnSeS quantum dots: an ultrasensitive fluorescence reporter in a conjugated molecular beacon system for the biosensing of influenza virus RNA (2016)

Controlling and engineering the particle composition of semiconductor alloys is one of the topmost targets in the field of semiconductor materials science and technology. Quantum dot (QD) nanocrystals offer an unmatched opportunity to obtain a wide range of composition-controlled alloys and have captivated a great deal of interest recently. Herein, we report on band gap engineering via tuning and controlling the sulphur molar fraction (ternary shell layer) of quaternary/ternary core/shell alloyed CdZnSeS/ZnSeS QDs. Varying optical properties were exhibited by the alloyed QDs but a uniform particle size distribution was maintained across all the compositions. The alloyed QDs displayed bright emission colours under UV irradiation, whereas the photoluminescence quantum yields (PL QY) were in a remarkable range of 36-98%. Non-linearity of the lattice parameter was an indication of gradient alloying of the nanocrystals, whereas the kinetics of the optical properties unravelled the effect of intrinsic optical bowing. Displacement of bond length and anion mismatch influenced the optical properties of the QDs with respect to the variation in the PL QY. Alloyed CdZnSeS/ZnSe<sub>1.0</sub>S<sub>1.3</sub> QDs with a spectacular PL QY were exploited as an ultrasensitive fluorescence reporter in a conjugated molecular beacon (MB) assay to detect influenza virus H1N1 RNA. Our detection system was rapid and highly sensitive for detecting extremely low concentrations of H1N1 RNA (down to 2 copies per mL), specific and versatile (detects H1N1 RNA in human serum). For proof of concept, the alloyed CdZnSeS/ZnSe<sub>1.0</sub>S<sub>1.3</sub> QD-MB bioprobe exhibited a superior 12-fold sensitivity over an alloyed CdZnSeS-MB probe, while a conventional CdSe/ZnS-MB probe could not detect extremely low concentrations of influenza virus H1N1 RNA.
Mechanical strain enhances survivability of collagen micronetworks in the presence of collagenase: implications for load-bearing matrix growth and stability (2009)

There has been great interest in understanding the methods by which collagen-based load-bearing tissue is constructed, grown and maintained in vertebrate animals. To date, the responsibility for this process has largely been placed with mesenchymal fibroblastic cells that are thought to fully control the morphology of load-bearing extracellular matrix (ECM). However, given clear limitations in the ability of fibroblastic cells to precisely place or remove single collagen molecules to sculpt tissue, we have hypothesized that the material itself must play a critical role in the determination of the form of structural ECM. We here demonstrate directly, using live, dynamic, differential interference contrast imaging, that mechanically strained networks of collagen fibrils, exposed to collagenase (Clostridium histolyticum), degrade preferentially. Specifically, unstrained fibrils are removed 'quickly', while strained fibrils persist significantly longer. The demonstration supports the idea that collagen networks are mechanosensitive in that they are stabilized by mechanical strain. Thus, collagen molecules (together with their complement enzymes) may comprise the basis of a smart, load-adaptive, structural material system. This concept has the potential to drastically simplify the assumed role of the fibroblast, which would need only to provide ECM molecules and mechanical force to sculpt collagenous tissue.
Role of N-linked glycans in the interaction between the envelope glycoprotein of human immunodeficiency virus and its CD4 cellular receptor. Structural enzymatic analysis. (1989)

gp120 and CD4 are two glycoproteins that are considered to interact together to allow the binding of HIV to CD4+ cells. We have utilized enzymatic digestion by endoglycosidases in order to analyze N-linked carbohydrate chains of these proteins and their possible role in the interaction of gp120 or gp160 with CD4. SDS denaturation was not necessary to obtain optimal deglycosylation of either molecule, but deglycosylation of CD4, nonetheless, depended on the presence of 1% Triton X-100. Endo H and Endo F that cleave high mannose type and biantennary glycans diminish the molecular mass of the glycoproteins from 120 or 160 Kd to 90 or 130 Kd, respectively; but these enzymes had no action on CD4 glycans. Endo F N-glycanase mixture, which acts on all glycan species, including triantennary chains, led to complete deglycosylation of gp120/160 and of CD4. Therefore, probably half of the glycan moieties of gp120/160 are composed of high mannose and biantennary chains, the other half being triantennary species. The carbohydrate structures of CD4 seems to be triantennary chains. To analyze the binding of gp120/160 to CD4, we used a molecular assay in which an mAb (110-4) coupled to Sepharose CL4B allowed the attachment of soluble gp120/160 to the beads; 125I-sCD4 was then added to measure the binding of CD4 to different amounts of gp120/160. Binding to gp160 was not modified when using completely deglycosylated 125I-sCD4, while deglycosylation of gp120 or of gp160 resulted in the decrease of the binding to native CD4 by two- and fivefold, respectively. Native and deglycosylated gp120/160 bound to CD4+ cells with comparable affinities. In addition, deglycosylated gp120 displaced 125I-gp160 binding to CD4+ cells and inhibited fusion of fresh Molt-T4 cells with CEM HIV1- or HIV2-infected cells to the same extent. Taken together, these results indicate that carbohydrates of CD4 and of gp120/160 do not play a significant role in the in vitro interaction between these two molecules.
Assessing detergent‐mediated virus inactivation, protein stability, and impurity clearance in biologics downstream processes (2022)

Detergent-mediated virus inactivation (VI) provides a valuable orthogonal strategy for viral clearance in mammalian processes, in particular for next-generation continuous manufacturing. Furthermore, there exists an industry-wide need to replace the conventionally employed detergent Triton X-100 with eco-friendly alternatives. However, given Triton X-100 has been the gold standard for VI due its minimal impact on protein stability and high inactivation efficacy, inactivation by other eco-friendly detergents and its impact on protein stability is not well understood. In this study, the sugar-based detergent commonly used in membrane protein purification, n-dodecyl-β- d-maltoside was found to be a promising alternative for VI. We investigated a panel of detergents to compare the relative VI efficacy, impact on therapeutic quality attributes, and clearance of the VI agent and other impurities through subsequent chromatographic steps. Detergent-mediated inactivation and protein stability showed comparable trends to low pH inactivation. Using experimental and modeling data, we found detergent-mediated product aggregation and its kinetics to be driven by extrinsic factors such as detergent and protein concentration. Detergent-mediated aggregation was also impacted by an initial aggregation level as well as intrinsic factors such as the protein sequence and detergent hydrophobicity, and critical micelle concentration. Knowledge gained here on factors driving product stability and VI provides valuable insight to design, standardize, and optimize conditions (concentration and duration of inactivation) for screening of detergent-mediated VI.
A dynamic programming algorithm for resolving transmit-ambiguities in the localization of WSN (2016)

In application cases where millimeter-sized (≤ 5mm diameter) sensor motes are inevitable to gather environmental data, the motes' inherent energy constraints require a radical change in the communication procedure. For application cases like the surveying of hardly permeable underground structures, as they exist e.g. in mining areas of oil sands, ten-thousands of miniature sensors are needed to examine e.g. the oil-resource wealth of the area. This combination of extremely resource limited sensor motes and the need to communicate with several ten-thousands of motes requires changes with respect to the normal communication procedure. As reducing the DS-CDMA code length, which is used for the identification of the motes, saves signification amount of energy, we consider the scenario where a localization of sensor motes is required by means of non-relatable distance measurements. The resulting ambiguities in the distance measurements are due to the reassigning of DS-CDMA codes. In this work, we consider the problem of re-enabling the localization, i.e. of resolving the ambiguities due to non-unique identification of the sensor motes, to allow classical localization algorithms to obtain a positioning of the motes. For this problem, which has already been shown to be NP-hard in general, we present an algorithm that is capable of solving this problem optimally in the maximum a posteriori sense. Further, we show that our algorithm offers significant complexity reductions for large problem instances.
Cross-Layer Optimization for Wireless Video Streaming &#8212; Performance and Cost (2005)

Cross-layer design (CLD) is a new paradigm for network architecture that allows us to make better use of network resources by optimizing across the boundaries of traditional network layers. Previous work has shown that applying CLD to mobile multimedia communication systems may lead to significant performance improvements. In this paper we also consider the other side of the coin, i.e., the additional computation and communication overhead introduced by CLD. We evaluate the performance improvements and the cost of cross-layer optimization using a wireless multi-user video streaming example.
σ-Bonded early transition metal–carbon derivatives. Part III. Complexes of methyltungsten(VI) pentahalide, halide oxide, and halide dioxide (1976)

Methyltungsten(VI) pentachloride has been obtained from WCl6 with HgMe2, and characterised by n.m.r. and i.r. spectroscopy. Reactions of WMeCl5 with bidentate ligands give WMeCl5·L adducts {L = Ph2P[CH2]2PPh2 or O[OP(NMe2)2]2}, while unidentate ligands give either extensive reduction [MeCN, SO(OMe)2, PO(OMe)3, or P(NMe2)3O] or chlorine–oxygen exchange reactions to WMeCl3O·L or WMeClO2·2L compounds [P(NMe2)3O, PPh3O, AsPh3O, or SMe2O]. Alkylation of WCl4O by HgMe2, ZnMe2, MgMe2, and MgMel has been investigated and shown to be dependent to a considerable extent on the solvent. The best results are obtained with MgMe2 in pentane containing 7% diethyl ether.
Eye contact sensing glasses for attention-sensitive wearable video blogging (2004)

We present ECSGlasses: eye contact sensing glasses that report when people look at their wearer. When eye contact is detected, the glasses stream this information to appliances to inform these about the wearer's engagement. We present one example of such an appliance, eyeBlog, a conversational video blogging system. The system uses eye contact information to decide when to record video from the glasses'; camera.
War of Words: The Competitive Dynamics of Legislative Processes (2020)

A body of law is an example of a dynamic corpus of text documents that are jointly maintained by a group of editors who compete and collaborate in complex constellations. Our goal is to develop predictive models for this process, thereby shedding light on the competitive dynamics of parliamentarians who make laws. For this purpose, we curated a dataset of 450000 legislative edits introduced by European parliamentarians over the last ten years. An edit modifies the status quo of a law, and could be in competition with another edit if it modifies the same part of that law. We propose a model for predicting the success of such edits, in the face of both the inertia of the status quo and the competition between overlapping edits. The parameters of this model can be interpreted in terms of the influence of parliamentarians and of the controversy of laws.
State Estimation of Thermal Systems with Multiple Operation Modes (2016)

The state estimation of thermal systems with multiple operation modes is considered. Based on a description as hybrid dynamical systems, we reduce it into an observer design problem for switched linear systems. In this design, a tradeoff between fast response and robustness must be taken into account in addition to a guarantee of stability as a switched system. For this purpose, we introduce LMIs with common Lyapunov function to place the closed-loop poles of the observer for each subsystem in the prescribed region in the complex plane. The effectiveness of proposed method is verified through numerical simulations with experimental data set.
jpHMM: Improving the reliability of recombination prediction in HIV-1 (2009)

Previously, we developed jumping profile hidden Markov model (jpHMM), a new method to detect recombinations in HIV-1 genomes. The jpHMM predicts recombination breakpoints in a query sequence and assigns to each position of the sequence one of the major HIV-1 subtypes. Since incorrect subtype assignment or recombination prediction may lead to wrong conclusions in epidemiological or vaccine research, information about the reliability of the predicted parental subtypes and breakpoint positions is valuable. For this reason, we extended the output of jpHMM to include such information in terms of 'uncertainty' regions in the recombination prediction and an interval estimate of the breakpoint. Both types of information are computed based on the posterior probabilities of the subtypes at each query sequence position. Our results show that this extension strongly improves the reliability of the jpHMM recombination prediction. The jpHMM is available online at http://jphmm.gobics.de/.
Impact of p16 Status and Anatomical Site in Anti-PD-1 Immunotherapy-Treated Recurrent/Metastatic Head and Neck Squamous Cell Carcinoma Patients (2021)

In head and neck squamous cell carcinoma (HNSCC), anti-PD-1 inhibitors are approved for recurrent/metastatic (R/M) disease and anticipated to expand to other indications. The impact of p16 status and anatomical site on overall survival (OS) in immunotherapy-treated HNSCC patients remains unresolved. We performed a retrospective analysis of R/M HNSCC patients receiving anti-PD-1 immunotherapy at our academic medical center with an extensive community satellite network. Fifty-three R/M HNSCC patients were treated with anti-PD-1 immunotherapy and had a median OS of 6 months. Anatomical site was associated with distinct OS; oropharynx and larynx patients have superior OS compared to oral cavity patients. Analysis of the OPSCC subset showed p16+ status as a favorable, independent prognostic biomarker (HR 7.67 (1.23-47.8); <i>p</i> = 0.029). Further studies to assess the link between anatomical site, p16 status, and anti-PD-1 treatment outcomes in large cohorts of R/M HNSCC patients managed in real-world clinical practices and clinical trials should be prioritized.
Conjugating Ligands to an Equilibrated Nanoparticle Protein Corona Enables Cell Targeting in Serum (2022)

Targeting ligands are conjugated onto nanoparticles to increase their selectivity for diseased cells. However, they become covered by serum proteins which prevent them from binding to target receptors. Here, we show that the nanoparticle protein corona achieved a maximum thickness in serum because the protein adsorption and desorption rates reached an equilibrium. Simulation experiments suggest that the number of molecular interactions between proteins decrease with distance from the nanoparticle surface until the forces are too weak to hold the proteins together. This results in an equilibration state between the proteins on the nanoparticle surface and in biological fluids. Conjugating targeting ligands to this equilibrated protein corona allowed the nanoparticles to bind to target cells in the presence of serum proteins. In contrast, conjugating targeting ligands directly to the nanoparticle surface resulted in a 55% reduction in binding to target cells in serum. We demonstrated this concept using two nanoparticle material types with different surface chemistries. We present a ligand-on-corona conjugation strategy that overcomes the negative impact of serum protein adsorption on nanoparticle cellular targeting.
Multi-process structuring of user interface software (1987)

Many contemporary user interface management systems suffer from the lack of adequate operating system support for multi-process structuring. They either adopt a single-process server approach, resulting in monolithic code, or are implemented as run-time libraries, resulting in a high degree of redundancy and complex synchronization problems. This paper, on the other hand, describes a methodology that takes advantage of lightweight processes and fast interprocess communication to structure user interface software as multiple cooperating processes. It demonstrates that such an approach can lead to exceptional flexibility -- with respect to the addition of new functionality, in particular -- without sacrificing performance.