gebhart/patrepeval huggingface dataset:
Probing the mechanical properties of brain cancer cells using a microfluidic cell squeezer device (2013)

Despite being invasive within surrounding brain tissues and the central nervous system, little is known about the mechanical properties of brain tumor cells in comparison with benign cells. Here, we present the first measurements of the peak pressure drop due to the passage of benign and cancerous brain cells through confined microchannels in a "microfluidic cell squeezer" device, as well as the elongation, speed, and entry time of the cells in confined channels. We find that cancerous and benign brain cells cannot be differentiated based on speeds or elongation. We have found that the entry time into a narrow constriction is a more sensitive indicator of the differences between malignant and healthy glial cells than pressure drops. Importantly, we also find that brain tumor cells take a longer time to squeeze through a constriction and migrate more slowly than benign cells in two dimensional wound healing assays. Based on these observations, we arrive at the surprising conclusion that the prevailing notion of extraneural cancer cells being more mechanically compliant than benign cells may not apply to brain cancer cells.
Impacts and solutions of nonvolatile-memory-induced weight error in the computing-in-memory neural network system (2020)

Abstract Nonvolatile-memory-based computing-in-memory architecture is one of the solutions to the massive data movement problem in the conventional von Neumann computing architecture since multiplication-and-accumulation (MAC) operations can be directly performed inside the memory array. This paper investigates the errors from the imperfections of resistive random access memory, including program error, read fluctuation and retention drift, and their impacts on the inference accuracy in convolutional neural network. The influences from weight errors in each convolution layer are evaluated according to the change of neuron distributions. A batch normalization (BN) parameter calibration method is proposed in order to correctly scale-and-shift the MAC results to compensate weight errors. This calibrated BN process drastically improves the inference accuracy not only for as-programmed analog ReRAM array but also for devices after longtime retention. This approach provides an effective direction to deal with the nonvolatile-memory-induced errors in artificial neural networks.
U-Net-based deep convolutional neural network for detection of superparamagnetic drug-eluting particles used for liver chemoembolization (2023)

Magnetic steering of superparamagnetic drug-eluting particles (SMDEPs) loaded with anti-tumor drugs across hepatic arteries is a promising technique to perform segmental liver embolization for patients with hepatocellular carcinomas (HCCs). These aggregates (20 &amp;plusmn; 6 SMDEPs) are sequentially released with a specially designed injector through a catheter in the proper hepatic artery of a swine placed in an MRI. Manual segmentation was previously done to localize and count the particles (volume of the artifact) in each lobe. We propose to train a U-net over this pre-existing database. Dice similarity coefficient, accuracy, and precision were respectively 99.1%, 98.3%, and 84.6%.
Holographic photoelectrochemical etching of diffraction gratings in n-InP and n-GaInAsP for distributed feedback lasers (1985)

Direct photoelectrochemical (PEC) etching of diffraction gratings on n-InP and n-GaInAsP in a 2-M HF/0.5-M KOH solution has been demonstrated using laser interference holography. Development of a maskless technique for producing gratings has potential application in the fabrication of distributed feedback lasers which are currently made by a multistep photoresist process. Submicron diffraction gratings having a period of 0.5 μm, corresponding to second-order feedback in GaInAsP at λ=1.55 μm, have been achieved. Measurements were obtained on the exposure characteristics, diffraction efficiency, and PEC etching sensitivity of gratings produced in InP and GaInAsP as a function of the writing beam intensity, laser wavelength, material doping level, and grating spatial frequency. For grating frequencies greater than 100 mm−1 the sensitivity was observed to decrease approximately as the inverse square of the spatial frequency. In addition, undoped InP and GaInAsP exhibited significantly lower sensitivities than n-doped material.
Attention Biasing and Context Augmentation for Zero-Shot Control of Encoder-Decoder Transformers for Natural Language Generation (2022)

Controlling neural network-based models for natural language generation (NLG) to realize desirable attributes in the generated outputs has broad applications in numerous areas such as machine translation, document summarization, and dialog systems. Approaches that enable such control in a zero-shot manner would be of great importance as, among other reasons, they remove the need for additional annotated data and training. In this work, we propose novel approaches for controlling encoder-decoder transformer-based NLG models in zero shot. While zero-shot control has previously been observed in massive models (e.g., GPT3), our method enables such control for smaller models. This is done by applying two control knobs, attention biasing and context augmentation, to these models directly during decoding and without additional training or auxiliary models. These knobs control the generation process by directly manipulating trained NLG models (e.g., biasing cross-attention layers). We show that not only are these NLG models robust to such manipulations but also their behavior could be controlled without an impact on their generation performance.
Nonlocal correlations between separated neural networks (2004)

In recent times the interest for quantum models of brain activity has rapidly grown. The Penrose-Hameroff model assumes that microtubules inside neurons are responsible for quantum computation inside brain. Several experiments seem to indicate that EPR-like correlations are possible at the biological level. In the past year , a very intensive experimental work about this subject has been done at DiBit Labs in Milan, Italy by our research group. Our experimental set-up is made by two separated and completely shielded basins where two parts of a common human DNA neuronal culture are monitored by EEG. Our main experimental result is that, under stimulation of one culture by means of a 630 nm laser beam at 300 ms, the cross-correlation between the two cultures grows up at maximum levels. Despite at this level of understanding it is impossible to tell if the origin of this non-locality is a genuine quantum effect, our experimental data seem to strongly suggest that biological systems present non-local properties not explainable by classical models.
Tumor necrosis factor increases the production of plasminogen activator inhibitor in human endothelial cells in vitro and in rats in vivo (1988)

The vascular endothelium plays an important role in fibrinolysis by producing tissue-type plasminogen activator (t-PA) and plasminogen activator inhibitor (PAI). The monokine tumor necrosis factor (human recombinant TNF) increased the production of PAI by cultured human endothelial cells from umbilical vein (twofold) and from foreskin microvessles (four to eight fold). This was demonstrated by titration of endothelial cell-conditioned medium with t-PA, by reverse fibrin autography, and by immunoprecipitation of [35S]PAI-1 by anti-PAI-1 IgG. TNF also induced a marked increase of PAI-1 messenger RNA (mRNA) in the cells. The stimulation of PAI activity by TNF was seen at 4 U/mL and reached a maximum at 500 U/mL. Human recombinant lymphotoxin and interleukin-1 (alpha and beta) also stimulated the production of PAI activity, while interleukin-6 was ineffective. Separate additions of TNF or interleukin-1 (IL-1) at optimal concentrations (500 U/mL and 5 U/mL, respectively) resulted in a comparable stimulation of PAI production by endothelial cells. The simultaneous addition of both mediators resulted in an additive effect. The effect of TNF could not be prevented by the addition of polymyxin B or by anti-IL-1 antibodies. Therefore, it is unlikely that TNF acts through the induction of IL-1 secretion by endothelial cells. Two hours after a bolus injection of 250,000 U/kg TNF into rats, a fivefold increase in circulating PAI levels was found. In the next ten hours, the levels returned to normal. Blood platelets do not significantly contribute to the increase in circulating PAI, because the number of platelets did not change after TNF injection and the amount of PAI in blood platelets is not sufficient for several hours during an increase in PAI activity. The acute phase reactants, fibrinogen and alpha 2-antiplasmin in rat plasma, were altered little if any two to 24 hours after injection of 250,000 U/kg TNF. In vitro, TNF did not change PAI production by human and rat hepatocytes in primary monolayer culture. Therefore, it is most likely that vascular endothelial cells contribute to the increased amount of circulating PAI induced by TNF in vivo. This increase in PAI activity might decrease fibrinolysis.
Separation of Nanocolloids by Taylor Cone Harmonics (2009)

The conducting Taylor cone can activate specified harmonics of Laplace equation near the cone and can generate field maxima at multiple discrete polar angles. As the nanocolloids are ejected out from the cone tip, the difference of dominating forces in axial and transverse direction defines size-dependent initial angle before the colloids are trapped by the field maxima of the harmonics at the closest polar angle. This size-dependent selection of harmonics governs the different size colloids to travel along different trajectories and form separated deposition in the downstream of the electrospray. This electrospray-based separation of nanocolloids is successfully used to detect DNA hybridization. A family of cone shape is generated by changing voltage in a finite range. Variation of Taylor cone angle changes the harmonics and the trajectory of colloid is found to shift to a larger polar angle under higher voltage.
Synthesis of Protected 3',5'-Di-2'-Deoxythymidine-(α-hydroxy-2-nitrobenzyl)-phosphonate Diesters as Dimer Building Blocks for Oligonucleotides (1995)

Abstract The synthesis of 3′-succinyl-CPG bound 3′,5′-di-2′-deoxythymidyl-(α-hydroxy-2-nitrobenzyl)-phosphonate diester 1 and the 3′-phosphoamidite derivative 2 is descibed. The hydroxyl-groups of the backbone modification were protected with trialkylsilyl groups: TES and TBS. Compounds 1, 2 are suitable blocks for oligonucleotide synthesis.
Hsp104 Catalyzes Formation and Elimination of Self-Replicating Sup35 Prion Conformers (2004)

The protein-remodeling factor Hsp104 governs inheritance of [PSI+], a yeast prion formed by self-perpetuating amyloid conformers of the translation termination factor Sup35. Perplexingly, either excess or insufficient Hsp104 eliminates [PSI+]. In vitro, at low concentrations, Hsp104 catalyzed the formation of oligomeric intermediates that proved critical for the nucleation of Sup 35 fibrillization de novo and displayed a conformation common among amyloidogenic polypeptides. At higher Hsp104 concentrations, amyloidogenic oligomerization and contingent fibrillization were abolished. Hsp104 also disassembled mature fibers in a manner that initially exposed new surfaces for conformational replication but eventually exterminated prion conformers. These Hsp104 activities differed in their reaction mechanism and can explain [PSI+] inheritance patterns.
Extraction and classification of graphical symbol candidates based on perceptual organization (2003)

A general-purpose graphical symbol extraction method is proposed in which the visual characteristics of graphical symbols are used. The graphical symbols are modeled as gatherings of short line segments and loops. Based on these models, two different methods are applied in parallel to a diagram, and two results are generated and integrated into the candidates. Further, a method to classify the extracted graphical symbol candidates by comparing their shape and structure is described. An important point of the method is that no a priori knowledge of the diagram under consideration is introduced, hence the method is applicable to a wide range of diagrams.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Altered immunoglobulin A and M levels associated with changes in BAFF and APRIL after administration of intravenous immunoglobulin to treat Kawasaki disease. (2010)

These results suggest that IVIG may affect the pathogenesis of KD through alteration of BAFF/APRIL.
Modeling of T2* decay in vertebral bone marrow fat quantification (2015)

Bone marrow fat fraction mapping using chemical shift encoding-based water-fat separation is becoming a useful tool in investigating the association between bone marrow adiposity and bone health and in assessing cancer treatment-induced bone marrow damage. Vertebral bone marrow is characterized by short T2* relaxation times, which are in general different for the water and fat components and can confound fat quantification. The purpose of the present study is to compare different approaches to T2* correction in chemical shift encoding-based water-fat imaging of vertebral bone marrow using single-voxel MRS as reference. Eight-echo gradient-echo imaging and single-voxel MRS measurements were made on the spine (L3-L5) of 25 healthy volunteers. Different approaches were evaluated for correction of T2* effects: (a) single-T2* correction, (b) dual-T2* correction, (c) T2' correction using the a priori-known T2 from the MRS at each vertebral body and (d) T2' correction using the a priori-known T2 equal to previously measured average values. Dual-T2* correction resulted in noisier imaging fat fraction maps than single-T2* correction or T2' correction using a priori-known T2. Linear regression analysis between imaging and MRS fat fraction showed a slope significantly different from 1 when using single-T2* correction (R(2) = 0.96) or dual-T2* correction (R(2) = 0.87). T2' correction using the a priori-known T2 resulted in a slope not significantly different from 1, an intercept significantly different from 0 (between 2.4% and 3%) and R(2) = 0.96. Therefore, a T2' correction using a priori-known T2 can remove the fat fraction bias induced by the difference in T2* between water and fat components without degrading noise performance in fat fraction mapping of vertebral bone marrow.
ChemInform Abstract: Fluorescent Amino Acids: Modular Building Blocks for the Assembly of New Tools for Chemical Biology (2013)

Abstract Review: 98 refs.
Biological Properties of Interferon‐α Produced Ex Vivo by Whole Blood of Patients Infected by Human Immunodeficiency Virus‐1 (1999)

We investigated the biological properties of interferon (IFN)-alpha produced by Sendai virus (SV)-activated whole blood cultures in 20 patients infected with human immunodeficiency virus (HIV)-1 and 24 healthy controls. Supernatants of cultures were assayed for IFN-alpha by using an immunological method (DELFIA), biological methods and an in-vitro MxA induction assay. The levels of intracellular MxA protein were detected by an immunochemiluminescence assay. The levels of IFN-alpha in patients measured by DELFIA were significantly lower than those in healthy controls (P < 0.0001), but the antiviral activity of IFN-alpha in patients infected with HIV-1 was lower than predicted from DELFIA. The IFN-alpha produced by cells of patients infected with HIV-1 was able to induce MxA protein in human amnions WISH cells but was unable to protect these cells against Vesicular Stomatitis Virus (VSV)-induced cytopathic effects. A relative increased capability to induce the production of MxA protein in vitro was observed with the IFN-alpha contained in culture supernatant of virus-activated whole blood of HIV-1-infected patients with increased levels of MxA in their peripheral blood. These data suggest that biological properties of IFN-alpha produced in the course of HIV-1 infection are different from those observed with IFN-alpha of healthy subjects.
Non-resonant elements with a simplified radiofrequency system for handset devices (2013)

Recent trends in handset antenna design are oriented to maximize the contribution of the ground plane to the radiation process. The challenge of these techniques mainly relies on the complexity of the radiofrequency system (combination of inductors, capacitors, and transmission lines) required to satisfy bandwidth and efficiency specifications. With the aim of simplifying this radiofrequency system, this paper proposes a new solution capable of minimizing the number of reactive components. The results demonstrate that the number of reactive elements can be reduced in a factor around three with respect to previous solutions while the electromagnetic performance is enhanced. Based on the proposed architecture, hepta-band operation for allocating eight communications standards GSM850, GSM900, GSM1800, GSM1900, UMTS, LTE2100, LTE2300, LTE2500 is achieved by means of two non-resonant elements of 5 mm × 5 mm × 5 mm and a radiofrequency system composed by only five reactive components.
Carbon–Foam Chromatographic Separation of Non-o,o´-Chlorine Substituted PCBs from Aroclor Mixtures (1980)

Abstract Columns of activated carbon dispersed on shredded polyurethane foam were used to separate non-o,o´-chlorine (Cl) substituted polychlorinated biphenyls (PCBs) from mg quantities of Aroclors 1016, 1242, 1248, 1254, and 1260. Aroclor 1248 contained the highest concentration (3400 μg/g) of highly toxic 3,4,3´,4´tetrachlorobiphenyl (TCB). Lesser amounts of 3,4,3’,4’-TCB were also found in Aroclors 1242 and 1254. However, we were unable to detect 3,4,3’,4’-TCB in Aroclors 1016 and 1260. Varying amounts of the non-o,o´-Cl substituted 3,4,4´-trichlorobiphenyl and 3,4,3´,4´,5´-pentachlorobiphenyl were found in most of the Aroclor mixtures. No residues of 3,4,5,3´,4´,5´-hexachlorobiphenyl were detected in the Aroclor mixtures examined. Using carbon-foam chromatography and high resolution capillary gas chromatography, 0.11 μg 3,4,3´,4´-TCB/g was detected in 3 subsamples of a composite of 5 carp from the Ohio River.
Abrupt gap formation in a linear lesion on the mitral isthmus (2010)

Recently, a novel linear multielectrode mapping/ablation catheter was developed. We present a case in which mitral isthmus line ablation was undertaken with this catheter and showed repeated conduction recovery at the same site on the line. Mapping with this multielectrode catheter along the whole lesion allowed recording of abrupt conduction resumption.
Stress dependent oxidation of sputtered niobium and effects on superconductivity (2014)

We report on the suppression of room temperature oxidation of DC sputtered niobium films and the effects upon the superconductive transition temperature, Tc. Niobium was sputter-deposited on silicon dioxide coated 150 mm wafers and permitted to oxidize at room temperature and pressure for up to two years. Resistivity and stress measurements indicate that tensile films greater than 400 MPa resist bulk oxidation with measurements using transmission electron microscope, electron dispersive X-ray spectroscopy, x-ray photoelectric spectroscopy, and secondary ion mass spectrometry confirming this result. Although a surface oxide, Nb2O5, consumed the top 6–10 nm, we measure less than 1 at. % oxygen and nitrogen in the bulk of the films after the oxidation period. Tc measurements using a SQUID magnetometer indicate that the tensile films maintained a Tc approaching the dirty superconductive limit of 8.4 K after two years of oxidation while maintaining room temperature sheet resistance. This work demonstrates that control over niobium film stress during deposition can prevent bulk oxidation by limiting the vertical grain boundaries ability to oxidize, prolonging the superconductive properties of sputtered niobium when exposed to atmosphere.
Dialect Recognition Using a Phone-GMM-Supervector-Based SVM Kernel: Presentation Slides (2010)

In this paper, we introduce a new approach to dialect recognition which relies on the hypothesis that certain phones are realized differently across dialects. Given a speaker’s utterance, we first obtain the most likely phone sequence using a phone recognizer. We then extract GMM Supervectors for each phone instance. Using these vectors, we design a kernel function that computes the similarities of phones between pairs of utterances. We employ this kernel to train SVM classifiers that estimate posterior probabilities, used during recognition. Testing our approach on four Arabic dialects from 30s cuts, we compare our performance to five approaches: PRLM; GMM-UBM; our own improved version of GMM-UBM which employs fMLLR adaptation; our recent discriminative phonotactic approach; and a state-of-the-art system: SDC-based GMM-UBM discriminatively trained. Our kernel-based technique outperforms all these previous approaches; the overall EER of our system is 4.9%.
Triggering a Cell Shape Change by Exploiting Preexisting Actomyosin Contractions (2020)

Apical constriction changes cell shapes, driving critical morphogenetic events including gastrulation in diverse organisms and neural tube closure in vertebrates. Apical constriction is thought to be triggered by contraction of apical actomyosin networks. We found that apical actomyosin contractions began before cell shape changes in both C. elegans and Drosophila. In C. elegans, actomyosin networks were initially dynamic, contracting and generating cortical tension without significant shrinking of apical surfaces. Apical cell-cell contact zones and actomyosin only later moved increasingly in concert, with no detectable change in actomyosin dynamics or cortical tension. Thus, apical constriction appears to be triggered not by a change in cortical tension but by dynamic linking of apical cell-cell contact zones to an already contractile apical cortex.
Biocompatible Lipid‐Coated Persistent Luminescent Nanoparticles for In Vivo Imaging of Dendritic Cell Migration (2019)

Abstract Dendritic cell (DC)‐based vaccines for immunotherapy have already achieved promising results in the last decade. To further improve current treatment protocols and enhance the therapeutic outcome, noninvasive in vivo tracking of DCs remains of crucial importance. Persistent luminescent nanoparticles (PLNPs) are inorganic materials which show an afterglow for hours after the optical excitation has ceased. If the afterglow is in the near‐infrared, the emission of injected particles can be tracked in vivo. However, stability and toxicity issues limit the use of bare PLNPs for biological applications. Therefore, appropriate surface functionalization is needed to improve their biocompatibility. In this study, it is demonstrated that near‐infrared light emitting LiGa 5 O 8 :Cr 3+ nanoparticles can be functionalized with a biocompatible lipid coating which provides them with outstanding stability in biological media. In vitro experiments show efficient uptake, absence of cytotoxicity even at very high particle concentrations, and no adverse effects on the maturation potential of DCs. DCs labeled with lipid‐coated LiGa 5 O 8 :Cr 3+ nanoparticles injected in mice can be imaged over days, confirming efficient in vivo migration to the popliteal lymph node. Together the results show that lipid coated LiGa 5 O 8 :Cr 3+ nanoparticles possess excellent possibilities for further use in research and development of DC based vaccines.
Fluorinated Graphene: Fluorinated Graphene in Interface Engineering of Ge‐Based Nanoelectronics (Adv. Funct. Mater. 12/2015) (2015)

The unstable germanium oxide formed at the interface between the channel and dielectric layer has impeded the progress of Ge-based nanoelectronics for more than 60 years. On page 1805, W. Ren, Z. Di, and co-workers integrate fluorinated graphene as an effective diffusion barrier layer to suppress the formation of unstable interfacial oxide between HfO2 gate oxide and Ge channel, thus obtaining the well-behaved Ge based MOS device with negligible C–V hysteresis, extremely low leakage, and superior equivalent oxide thickness.