gebhart/patrepeval huggingface dataset:
Sorting of particles suspended in whole blood (2019)

An important step in diagnostics is the isolation of specific cells and microorganisms of interest from blood. Since such bioparticles are often present at very low concentrations, throughput needs to be as high as possible. In addition, to ensure simplicity, a minimum of sample preparation is important. Therefore, sorting schemes that function for whole blood are highly desirable. Deterministic lateral displacement (DLD) has proven to be very precise and versatile in terms of a wide range of sorting parameters. To better understand how DLD performs for blood as the hematocrit increases, we have performed measurements and simulations for spherical particles in the micrometer range moving through DLD arrays for different flow velocities and hematocrits ranging from pure buffer to whole blood. We find that the separation function of the DLD array is sustained, even though blood cells introduce a shift in the trajectories and a significant dispersion for particles that are close to the critical size in the device. Simulations qualitatively replicate our experimental observations and help us identify fundamental mechanisms for the effect of hematocrit on the performance of the DLD device.
Biological Lignin Valorization (2022)

Given lignin's heterogeneity, catalytic depolymerization results in aromatic compound mixtures, and conversion of this complex substrate to a single product is challenging. To that end, the Biological Lignin Valorization (BLV) project is pursuing biological funneling, wherein aromatic catabolic microbes are engineered to convert a mixture of lignin-derived compounds to a single product. Namely, we employ Pseudomonas putida and pursue atom-efficient products, such as muconic acid, which can be further converted to direct replacements or used in performance-advantaged bioproducts. Overall, biological lignin conversion can make major contributions to reduce the minimum fuel selling price of the integrated biorefinery. Early industrial efforts in this area are also leading to value-added products, including in collaboration with the BLV project. Primary challenges associated with BLV efforts include accessing bio-available monomers from lignin (with the Lignin Utilization project), enabling commercial titers, rates, and yields of bioproducts from lignin-derived compounds, and overcoming substrate and product toxicity. To date, we have 1) demonstrated 49 g/L of muconate from aromatic compounds and 4 g/L of muconate from lignin, 2) improved the toxicity tolerance of P. putida to key aromatic substrates, 3) debottlenecked biological funneling for higher rates, and 4) engineered P. putida to convert S, G, and H-type lignin-derived compounds to a single product.
Spatio-temporal optical random number generator (2015)

We present a first random number generator (RNG) which simultaneously uses independent spatial and temporal quantum randomness contained in an optical system. Availability of the two independent sources of entropy makes the RNG resilient to hardware failure and signal injection attacks. We show that the deviation from randomness of the generated numbers can be estimated quickly from simple measurements thus eliminating the need for usual time-consuming statistical testing of the output data. As a confirmation it is demonstrated that generated numbers pass NIST Statistical test suite.
Solution-Processed Zinc Oxide Field-Effect Transistors Based on Self-Assembly of Colloidal Nanorods (2005)

Colloidal zinc oxide (ZnO) nanocrystals are attractive candidates for a low-temperature and solution-processible semiconductor for high-performance thin-film field-effect transistors (TFTs). Here we show that by controlling the shape of the nanocrystals from spheres to rods the semiconducting properties of spin-coated ZnO films can be much improved as a result of increasing particle size and self-alignment of the nanorods along the substrate. Postdeposition hydrothermal growth in an aqueous zinc ion solution has been found to further enhance grain size and connectivity and improve device performance. TFT devices made from 65-nm-long and 10-nm-wide nanorods deposited by spin coating have been fabricated at moderate temperatures of 230 degrees C with mobilities of 0.61 cm(2)V(-1)s(-1) and on/off ratios of 3 x 10(5) after postdeposition growth, which is comparable to the characteristics of TFTs fabricated by traditional sputtering methods.
Tissu adipeux et cancer (2014)

Adipose tissue is found in close proximity whith many invasive cancers. In breast cancer, early local tumour invasion results in close interactions of cancer cells with fully differentiated adipocytes. Aside from their energy-storing function, mature adipocytes are also active endocrine cells prone to influence tumour behaviour through heterotypic signaling processes. After a short description of anatomical depots specificities of adipose tissue, we describe the phenotypic changes induced by tumor secretion in tumour-surrounding adipocytes. These cells (that we named CAA for cancer-associated adipocytes) by their ability to secrete pro-inflammatory cytokines, extra-cellular matrix proteins and proteases involved in its remodeling, as well as to release free fatty acid, stimulate tumor proliferation, invasiveness and drug resistance. These results support the concept that adipocytes participate in a deleterious crosstalk with cancer cells to support tumour progression, that might be amplified in obesity conditions and explain the poor prognosis of cancers observed in this subset of patients.
Distributional lexical semantics: Toward uniform representation paradigms for advanced acquisition and processing tasks (2010)

The distributional hypothesis states that words with similar distributional properties have similar semantic properties (Harris 1968). This perspective on word semantics, was early discussed in linguistics (Firth 1957; Harris 1968), and then successfully applied to Information Retrieval (Salton, Wong and Yang 1975). In Information Retrieval, distributional notions (e.g. document frequency and word co-occurrence counts) have proved a key factor of success, as opposed to early logic-based approaches to relevance modeling (van Rijsbergen 1986; Chiaramella and Chevallet 1992; van Rijsbergen and Lalmas 1996).
EFloat: Entropy-coded Floating Point Format for Compressing Vector Embedding Models (2021)

In a large class of deep learning models, including vector embedding models such as word and database embeddings, we observe that floating point exponent values cluster around a few unique values, permitting entropy based data compression. Entropy coding compresses fixed-length values with variable-length codes, encoding most probable values with fewer bits. We propose the EFloat compressed floating point number format that uses a variable field boundary between the exponent and significand fields. EFloat uses entropy coding on exponent values and signs to minimize the average width of the exponent and sign fields, while preserving the original FP32 exponent range unchanged. Saved bits become part of the significand field increasing the EFloat numeric precision by 4.3 bits on average compared to other reduced-precision floating point formats. EFloat makes 8-bit and even smaller floats practical without sacrificing the exponent range of a 32-bit floating point representation. We currently use the EFloat format for saving memory capacity and bandwidth consumption of large vector embedding models such as those used for database embeddings. Using the RMS error as metric, we demonstrate that EFloat provides higher accuracy than other floating point formats with equal bit budget. The EF12 format with 12-bit budget has less end-to-end application error than the 16-bit BFloat16. EF16 with 16-bit budget has an RMS-error 17 to 35 times less than BF16 RMS-error for a diverse set of embedding models. When making similarity and dissimilarity queries, using the NDCG ranking metric, EFloat matches the result quality of prior floating point representations with larger bit budgets.
Circulating interleukin-1 and tumor necrosis factor antagonists in liver disease (1993)

The proinflammatory cytokines interleukin-1 and tumor necrosis factor-alpha are thought to play important roles in the pathophysiology of liver disease. Specific antagonists of these cytokines have been found in recent years. Interleukin-1 receptor antagonist is a specific interleukin-1 antagonist. The soluble receptor derived from the cell-surface p55 tumor necrosis factor receptor p55 is a naturally occurring substance that inhibits the biological effects of tumor necrosis factor. We used specific radioimmunoassays to detect circulating interleukin-1 receptor antagonist and tumor necrosis factor soluble receptor p55 levels in 14 patients with acute viral hepatitis and in 160 patients with various chronic liver diseases. Levels of interleukin-1 receptor antagonist and, especially, tumor necrosis factor soluble receptor were markedly increased in most patients with chronic liver disease regardless of pathogenesis and in viral hepatitis. Patients with chronic liver disease and cirrhosis showed significantly higher levels of both cytokine antagonists than did noncirrhotic patients. Correlations between interleukin-1 receptor antagonist and tumor necrosis factor soluble receptor were more significant than those of either antagonist with C-reactive protein or blood sedimentation rate. Interleukin-1 receptor antagonist and tumor necrosis factor soluble receptor levels were also positively correlated with bilirubin and AST levels. We conclude that circulating levels of interleukin-1 receptor antagonist and tumor necrosis factor soluble receptor may reflect ongoing disease activity and probably modulate some effects of endogenous interleukin-1 and tumor necrosis factor.
Urban structure classification using the 3D normal distribution transform for practical robot applications (2013)

Previous urban structure classification methods are intractable for practical robots in two viewpoints: storing point clouds and complex computation for using conditional random fields. This paper presents a classification method based on normal distribution transform (NDT) grids for practical robots. NDT grids store point clouds in the form of the mean and covariance, instead of directly dealing with huge point clouds. By taking the advantage of NDT grids, we design geometric-featured voxel (GFV) based on NDT grids to represent urban structures as a voxel model. The proposed method consists of three steps: GFV generation, segmentation, and classification. In the segmentation, GFVs are clustered according to units of urban structures by spectral clustering. For the classification, the clustered GFVs are classified as one kind of urban structures by supervised learning. Geometric characteristics of urban structures are expressed by a histogram of geometric words. Experimental results prove that the proposed method based on NDT grids is suitable for practical robots in terms of memory requirement, computation time, and even classification accuracy.
Broadband fiber lasers (1988)

Miniature broadband optical sources are of interest for fiber-optic gyroscopes to reduce coherent errors due to backscattering and polarization coupling. As an alternative to superluminescent diodes (SLDs), which suffer from a 300–400-ppm/°C wavelength sensitivity to temperature and spectrum sensitivity to feedback, two new types of 1060-nm broadband source involving an optically pumped Nd-doped fiber have been developed. The first relies on superfluorescence emission in a fiber provided with a high reflector on the pump input end. The onset of superfluorescence threshold was observed at P abs ~ 70 mW, a pump power level which can be provided by a high power laser diode array. The second source is a resonant fiber laser which utilizes the inhomogeneous nature of the Nd 3+ electronic transitions to produce a broad emission bandwidth. This fiber laser involves one high reflector bonded at each end and exhibits a much lower threshold ( P abs = 1–2 mW). With a 30-mW diode laser as a pump, a 2.5-mW output signal with a 19-nm bandwidth was observed. As expected from the thermal stability of the host, both sources exhibit a tenfold increase in spectrum stability with temperature over SLDs.
Compact 2.4-/2.9-GHz band parallel-planar bandpass filter (2009)

This paper proposes a compact dual-band bandpass filter (DBPF) based on a parallel-planar architecture where resonators are formed on the opposite sides of each substrate. The proposed architecture enables dual-band operation without an appreciable change in the volume of the DBPF and yields design freedom for the resonant frequencies by adjusting the distance between the substrates. A 2.4-/2.9-GHz band DBPF is fabricated using YBCO film deposited on a MgO substrate with a coplanar waveguide structure to investigate experimentally dual-band operation. The measurement results agree with those of the simulation.
A good death? (2019)

This paper offers some personal reflections on the idea of ‘a good death’, a theme in the writing of philosophers since classical times. The hospice movement has made immense progress in creating conditions in which we can ‘die better’. But such experiences are still the exception rather than the rule. The psychological challenge is how to relate to the dying as they are dying, and how as we die we relate to the living. I reflect on my own experience of my father's death, and a moment of fleeting but genuine contact between us. Atul Gawande's idea of the ‘hard conversations’ we must learn to have as we approach death are enlightening. Ultimately I argue, we die alone, and how we are, or are not, ‘held in mind’ as we approach death may be an index of the nearest we can approach to the idea of an ‘afterlife’.
Application and Commercial Prospects of Fullerenes in Medicine and Biology (2005)

C Sixty Inc. is a private biopharmaceutical company focusing on the discovery and the development of a new class of therapeutics based on the fullerene molecule, a hollow sphere made up of 60 carbon atoms which was discovered in 1985 as the third and unprecedented new form of elemental carbon in nature. It was dubbed buckminsterfullerene (or fullerene) because of its geodesic character and its discoverers were awarded the 1996 Nobel Prize in chemistry. C Sixty’s lead products are based on modification of the fullerene molecule and include advanced products for the treatment of cancer, AIDS and neurodegenerative diseases. The company is also committed to a research, development and discovery program of novel biopharmaceuticals, diagnostics and medical devices for applications in diverse disease categories based on the unique molecular pincushion platform of the fullerene molecule. The company has a diverse proprietary intellectual portfolio which includes 5 issued and 3 new patent applications. The founding scientists of C Sixty Inc. include the undisputed world leaders in the application of fullerene to medicine, including the 1996 Nobel Prize winners in chemistry.
Gene expression analysis using a highly sensitive DNA microarray for colorectal cancer screening. (2014)

Gene profiling assay using a highly sensitive DNA chip was more effective than FOBT at detecting patients with small, right-sided, surface tumor, and early-stage CRC.
P4‐576: CONCORDANCE BETWEEN 18F‐PI‐2620 TAU PET/MRI IMAGING AND CLINICAL OUTCOMES IN ALZHEIMER DISEASE AND OTHER TAUOPATHIES (2019)

Primary pathology of Alzheimer disease (AD) includes both β-amyloid and neurofibrillary tangles (NFT) of misfolded tau. Diagnosing tau pathology in vivo and correlating with clinical status is crucial in diagnosis and development of anti-tau therapy. The goal of this study was to 1) create a clinical protocol for evaluating a novel Tau PET ligand, 18F-PI-2620, 2) evaluate concordance between radiologists, and 3) compare to clinical status and quantified SUVR. Per Braak staging, NFTs start in the entorhinal cortex (Braak 1–2), progress to the hippocampus (Braak 3–4) and lastly impact neocortex (Braak 5–6). Criteria for tau positivity was based on modified Braak staging, where Braak stages 1&2, 3&4, and 5&6 were collapsed into stage A, B, and C, respectively, with no uptake staged as 0. Positivity was determined based on visual uptake greater than off-target regions. Two physicians were blinded to patient status, and independently evaluated fused PET/MRI for 16 healthy older controls and 12 patients with MCI or dementia. Using non-parametric Wilcoxin signed rank tests, visual ratings were then compared to SUVR from medial and lateral temporal ROIs. Of the 16 healthy controls, 12, 1, 2, and 1 participants were classified as 0, A, B, and C, respectively. All 3 MCI patients were classified C. One AD patient was classified as A, while 4 others were C. Of the other tauopathies, one patient with semantic dementia was classified as stage C. There was 89.2% agreement rate between radiologists (Cohen's kappa coefficient of 0.78, standard error=0.12). Significantly elevated SUVRs were present in individuals with some binding (stage A-C) compared to individuals with no binding (stage 0). The greatest disagreement was for intermediate levels corresponding to Braak 3-4. Off target uptake included the substantia nigra, venous and nasal sinuses, and choroid plexuses.
Efficient Poling of Electro‐Optic Polymers in Thin Films and Silicon Slot Waveguides by Detachable Pyroelectric Crystals (2011)

Pyroelectric crystals are used as a conformal and detachable electric field source to efficiently pole electro-optic (E-O) polymers in both parallel-plate (transverse) and in-plane (quasi-longitudinal) configurations. Large Pockels coefficients in poled thin films and high tunability of resonance wavelength shift in hybrid polymer silicon slot waveguide ring-resonator modulators have been achieved using this method.
Multiple reaction monitoring mass spectrometry for the discovery of environmentally modulated proteins in an aquatic invertebrate sentinel species, Gammarus fossarum (2022)

Multiple reaction monitoring (MRM) mass spectrometry is emerging as a relevant tool for measuring customized molecular markers in freshwater sentinel species. While this technique is typically used for the validation of protein molecular markers preselected from shotgun experiments, recent gains of MRM multiplexing capacity offer new possibilities to conduct large-scale screening of animal proteomes. By combining the strength of active biomonitoring strategies and MRM technologies, this study aims to propose a new strategy for the discovery of candidate proteins that respond to environmental variability. For this purpose, 249 peptides derived from 147 proteins were monitored by MRM in 273 male gammarids caged in 56 environmental sites, representative of the diversity of French water bodies. A methodology is here proposed to identify a set of customized housekeeping peptides (HKPs) used to correct analytical batch effects and allow proper comparison of peptide levels in gammarids. A comparative analysis performed on HKPs-normalized data resulted in the identification of peptides highly modulated in the environment and derived from proteins likely involved in the environmental stress response. Overall, this study proposes a breakthrough approach to screen and identify potential proteins responding to relevant environmental conditions in sentinel species.
Ultrastructural Changes in the Compound Middle Lamella of Pinus thunbergii During Lignification and Lignin Removal (2000)

Summary The structure of the middle lamella in Pinus thunbergii has been studied by the rapid-freeze deep-etching (RFDE) technique in combination with transmission electron microscopy (TEM). The ultrastructure of the compound middle lamella was studied in the early phases of the development of woody tissue in the cambial and differentiating xylem, before the heavy incrustation with lignin had occurred. Lignified middle lamella in the xylem was studied both directly and after delignification. It was found that the structure of the unlignified middle lamella in the cambium/developing xylem consists of a fine irregular network probably containing pectin and hemicellulose. As a result of lignin incrustation, the middle lamella becomes increasingly dense and the surface structure of the fully lignified middle lamella appeared to be compact and partly covered with globular structures. After delignification of the lignified middle lamella a thin network with a different structure was revealed. This network probably mainly consists of hemicellulose. No microfibrils of the type that occurs in the primary and secondary walls were found in the middle lamella.
Novel adaptive predistortion technique for cross coupled filters (2003)

This paper presents a novel adaptive predistortion technique for general cross-coupled microwave/RF filters with improved insertion loss and group delay equalization. The method enables many potential applications of an almost abandoned technique, especially using a lower Q design to emulate the performance of a higher Q filter. A 10-4-4 coaxial filter was built to verify the validity of the new method. The technique should lead to practical applications such as satellite transponder input multiplexers.
Age-related compensation: Neuromusculoskeletal capacity, reserve & movement objectives. (2021)

The prevention, mitigation and treatment of movement impairments, ideally, requires early diagnosis or identification. As the human movement system has physiological and functional redundancy, movement limitations do not promptly arise at the onset of physical decline. A such, prediction of movement limitations is complex: it is unclear how much decline can be tolerated before movement limitations start. Currently, the term 'homeostatic reserve' or 'physiological reserve' is used to refer to the redundancy of the human biological system, but these terms do not describe the redundancy in the muscle architecture of the human body. The result of functional redundancy is compensation. Although compensation is an early predictor of movement limitations, clear definitions are lacking and the topic is underexposed in literature. The aim of this article is to provide a definition of compensation and emphasize its importance. Compensation is defined as an alteration in the movement trajectory and/or altering muscle recruitment to complete a movement task. Compensation for capacity is the result of a lack in neuromusculoskeletal reserve, where reserve is defined as the difference between the capacity (physiological abilities of the neuromusculoskeletal system) and the task demand. Compensation for movement objectives is a result of a shift in weighting of movement objectives, reflecting changing priorities. Studying compensation in biomechanics requires altered protocols in experimental set-ups, musculoskeletal models that are not reliant on prescribed movement, and inclusion of alternative movement objectives in optimal control theory.