gebhart/patrepeval huggingface dataset:
Deficiency of retinoblastoma protein leads to inappropriate S-phase entry, activation of E2F-responsive genes, and apoptosis. (1995)

The retinoblastoma susceptibility gene (Rb) participates in controlling the G1/S-phase transition, presumably by binding and inactivating E2F transcription activator family members. Mouse embryonic fibroblasts (MEFs) with no, one, or two inactivated Rb genes were used to determine the specific contributions of Rb protein to cell cycle progression and gene expression. MEFs lacking both Rb alleles (Rb-/-) entered S phase in the presence of the dihydrofolate reductase inhibitor methotrexate. Two E2F target genes, dihydrofolate reductase and thymidylate synthase, displayed elevated mRNA and protein levels in Rb- MEFs. Since absence of functional Rb protein in MEFs is sufficient for S-phase entry under growth-limiting conditions, these data indicate that the E2F complexes containing Rb protein, and not the Rb-related proteins p107 and p130, may be rate limiting for the G1/S transition. Antineoplastic drugs caused accumulation of p53 in the nuclei of both Rb+/+ and Rb-/- MEFs. While p53 induction led to apoptosis in Rb-/- MEFs, Rb+/- and Rb+/+ MEFs underwent cell cycle arrest without apoptosis. These results reveal that diverse growth signals work through Rb to regulate entry into S phase, and they indicate that absence of Rb protein produces a constitutive DNA replication signal capable of activating a p53-associated apoptotic response.
The NP9 protein encoded by the human endogenous retrovirus HERV‐K(HML‐2) negatively regulates gene activation of the Epstein‐Barr virus nuclear antigen 2 (EBNA2) (2010)

Epstein-Barr virus (EBV) is a human tumour virus that efficiently growth-transforms primary human B-lymphocytes in vitro. The viral nuclear antigen 2 (EBNA2) is essential for immortalisation of B-cells and stimulates viral and cellular gene expression through interaction with DNA-bound transcription factors. Like its cellular homologue Notch, it associates with the DNA-bound repressor RBPJκ (CSL/CBF1) thereby converting RBPJκ into the active state. For instance, both EBNA2 and Notch activate the cellular HES1 promoter. In EBV-transformed lymphocytes, the RNA of the NP9 protein encoded by human endogenous retrovirus HERV-K(HML-2) Type 1 is strongly up-regulated. The NP9 protein is detectable both in EBV-positive Raji cells, a Burkitt's lymphoma cell line, and in IB4, an EBV-transformed human lymphoblastoid cell line. NP9 binds to LNX that forms a complex with the Notch regulator Numb. Therefore, the function of NP9 vis-à-vis Notch and EBNA2 was analysed. Here, we show that NP9 binds to EBNA2 and negatively affects the EBNA2-mediated activation of the viral C- and LMP2A promoters. In contrast, NP9 did neither interfere in the activation of the HES1 promoter by Notch nor the induction of the viral LMP1 promoter by EBNA2. In an electrophoretic mobility shift analysis, NP9 reduced the binding of EBNA2 to DNA-bound RBPJκ by about 50%. The down-regulation of EBNA2-activity by NP9 might represent a cellular defence mechanism against viral infection or could, alternatively, represent an adaptation of the virus to prevent excessive viral protein production that might otherwise be harmful for the infected cell.
Recruitment of effector lymphocytes by initiator lymphocytes. Circulating lymphocytes are trapped in the reacting lymph node. (1976)

In previous studies, we have shown that initiator T lymphocytes (ITL) sensitized in vitro recruit effector T lymphocytes in vivo. When ITL were sensitized against fibroblast antigens in vitro and injected into footpads of syngeneic recipients, they induced enlargement of the draining popliteal lymph node (PLN) and the development there of specific effector lymphocytes of recipient origin. To study the basis of this lymph node response in recruitment, we injected 51Cr-labeled spleen cells i.v. into recipients of sensitized ITL and found that the labeled circulating lymphocytes were trapped in the reacting PLN. The trapping depended on surface properties of the labeled circulating lymphocytes, as revealed by various enzymatic treatments. The trapping process was radiosensitive, both on the part of the trapped lymphocytes and the lymph node-trapping mechanism. Thus, sensitized ITL injected into the hind footpads migrate to the PLN and induce the trapping of circulating recruitable lymphocytes, which either differentiate into or regulate the differentiation of effector T lymphocytes.
Ligand Exchange of Au25SG18 Leading to Functionalized Gold Clusters: Spectroscopy, Kinetics, and Luminescence (2008)

Ligand exchange offers an effective way to modify the properties of the recently prepared quantum clusters of gold. To tune optical and photoluminescence properties of one of the most stable quantum clusters of gold, Au25SG18 (SG-glutathione thiolate), we functionalized it by the exchange of −SG with functionalized -SG and with an altogether different ligand, namely, 3-mercapto-2-butanol (MB). The products were characterized by various techniques such as optical absorption (UV−vis), Fourier-transform infrared (FT-IR), nuclear magnetic resonance (NMR), X-ray photoelectron (XPS), and luminescence spectroscopies, mass spectrometry, and thermogravimetry (TG). Analyses of the TG data helped to establish the molecular composition of the products. Ligand exchange reaction was monitored by NMR spectroscopy, and it was found that the exchange reaction follows a first order kinetics. The XPS study showed that after the exchange reaction there was no change in the chemical nature of the metal core and binding energy values of Au 4f7/2 and 4f5/2, which are similar in both the parent and the exchanged products. Photoluminescence studies of these clusters, done in the aerated conditions, showed that the excitation spectrum of the MB-exchanged product is entirely different from the acetyl- and formyl-glutathione exchanged products. The inherent fluorescence and solid-state emission of these clusters were observed. This intense emission allows optical imaging of the material in the solid state. The emission is strongly temperature dependent. The synthesis of a diverse variety of clusters and their chemical stability and intense luminescence offer numerous applications in areas such as energy transfer, sensors, biolabeling, and drug delivery.
Maize SBP-box transcription factors unbranched2 and unbranched3 affect yield traits by regulating the rate of lateral primordia initiation (2014)

The separation of male and female flowers in maize provides the potential for independent regulation of traits that affect crop productivity. For example, tassel branch number controls pollen abundance and length of shedding time, whereas ear row number directly affects kernel yield. Mutations in duplicate SBP-box transcription factor genes unbranched2 (ub2) and ub3 affect both of these yield traits. Double mutants display a decrease in tassel branch number and an increase in ear row number, both of which are enhanced by loss of a related gene called tasselsheath4 (tsh4). Furthermore, triple mutants have more tillers and leaves-phenotypes seen in Corngrass1 mutants that result from widespread repression of SBP-box genes. Immunolocalization of UB2 and UB3 proteins revealed accumulation throughout the meristem but absence from the central domain of the meristem where cells regenerate. Thus, ub2, ub3, and tsh4 function as redundant factors that limit the rate of cell differentiation to the lateral domains of meristems. When these genes are mutated, cells are allocated to lateral primordia at a higher rate, causing a net loss of cells from the central domain and premature termination of the inflorescence. The ub3 locus is tightly linked to quantitative trait loci (QTL) for ear row number and tassel branch number in both the nested association mapping (NAM) and intermated B73 by Mo17 (IBM) populations of maize recombinant inbreds, indicating that this gene may be agronomically important. Analysis of ear and tassel QTL across biparental families suggests that multiple mutations in ub3 independently regulate male and female inflorescence development.
Is one-way modal conversion sufficient for optical isolation (2011)

We show that the novel one-way photonic modal conversion effect, as demonstrated by Feng et al (Reports, 11 August, 2011, p. 729), is insufficient in itself to enable optical isolation, since the underlying dielectric structure possesses a symmetric scattering matrix. Moreover, one cannot construct an optical isolator, by enclosing this structure with a system containing any combination of components or signal processing elements, as long as the overall system is linear, and is described by a static scalar dielectric function. Instead, to achieve complete optical isolation, one would need to augment the present design so that the final system is described by a non-symmetric scattering matrix.
Influence of animal host and tumor implantation site on radio‐antibody uptake in the GW‐39 human colonic cancer xenograft (1989)

The magnitude and kinetics of tumor uptake of a monoclonal antibody (MAb) directed against carcinoembryonic antigen (CEA) in the GW-39 human colorectal cancer xenograft differ according to the animal used (nude mouse or hamster) and the site of implantation of the tumor within the animal (cheek pouch, leg muscle, subcutaneous or liver). Several physiological factors have been evaluated in an attempt to explain these differences in radio-antibody accumulation. The following observations have been made: (1) The animal host with the slower blood clearance of radio-antibody and the higher non-tumor tissue uptake has the higher tumor uptake; (2) the xenografts with a higher blood-flow rate, vascular volume and/or vascular permeability have a higher specific radio-antibody targeting; (3) the smaller, more viable tumors take up more radio-antibody per gram than the larger tumors; and (4) tumors with higher specific antigen content accrete more radio-antibody. These results are discussed in terms of the feasibility of clinical tumor imaging and therapy with radiolabelled antibodies.
Supplementary Movie 1 from Targeting uPAR with Antagonistic Recombinant Human Antibodies in Aggressive Breast Cancer (2023)

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Fatal Chest Injury by Baseball Impact in Children (1992)

Each year several children die as a result of baseball impact to the chest. This review describes the circumstances of 24 deaths from 1973 to 1983 and suggests the development of approaches to prevent and better treat the injuries. These approaches include the development of both an experimental animal model that mimics the physiologic mechanism of death from chest impact and the use of test dummies to evaluate the effectiveness of sport equipment in minimizing impact forces. Both of these developments would contribute to a reduction of the injury risks in children hit by a baseball. This review also examines the possible role of current cardiopulmonary resuscitation procedures in the outcome of the 24 recorded deaths and suggests possible changes to resuscitation protocols. Particularly the use of the precordial thump.
Abstract B046: Multimodal biomarkers that predict the presence of Gleason pattern 4: Potential impact for active surveillance (2023)

Abstract Purpose: Latent Grade Group (GG) ≥2 prostate cancer can impact the performance of active surveillance (AS) protocols. To date, molecular biomarkers for AS have relied solely on RNA or protein. We trained and independently validated multimodal (mRNA abundance, DNA methylation, and DNA copy number) biomarkers that more accurately separate GG1 from GG≥2 cancers. Materials and Methods: Low- and intermediate-risk prostate cancer patients were assigned to training (n=333) and validation (n=202) cohorts. We profiled the abundance of 342 mRNAs, 100 DNA copy number aberration (CNA) loci and 14 hypermethylation sites at two locations per tumor. Using the training cohort with cross- validation, we evaluated methods for training classifiers of pathologic GG≥2 in centrally reviewed radical prostectomies (RPs). We trained two distinct classifiers, PRONTO-e and PRONTO-m, and validated them in an independent RP cohort. Results: PRONTO-e comprises 353 mRNA and CNA features. PRONTO-m includes 94 clinical, mRNAs, CNAs and methylation features at 14 and 12 loci, respectively. In independent validation, PRONTO-e and PRONTO-m predicted GG≥2 with respective true positive rates of 0.81 and 0.76, false positive rates of 0.43 and 0.26. Both classifiers were resistant to sampling error and identified more upgraded men than a well-validated pre-surgical risk calculator, CAPRA (p &amp;lt;0.001). Conclusions: Two GG classifiers with superior accuracy were developed by incorporating RNA and DNA features and validated in an independent cohort. Upon further validation in biopsy samples, classifiers with these performance characteristics could refine selection of men for AS, extending their treatment-free survival and intervals between surveillance. Citation Format: Anna Y. Lee, David M. Berman, Robert Lesurf, Palak G. Patel, Walead Ebrahimizadeh, Jane Bayani, Laura A. Lee, Nadia Boufaied, Shamini Selvarajah, Tamara Jamaspishvili, Karl-Philippe Guérard, Dan Dion, Atsunari Kawashima, Gina M. Clarke, Nathan How, Chelsea L. Jackson, Eleonora Scarlata, Khurram Siddiqui, John B.A. Okello, Armen G. Aprikian, Madeleine Moussa, Antonio Finelli, Joseph Chin, Fadi Brimo, Glenn Bauman, Andrew Loblaw, Vasundara Venkateswaran, Ralph Buttyan, Simone Chevalier, Axel Thomson, Paul C. Park, D. Robert Siemens, Jacques Lapointe, Paul C. Boutros, John M.S. Bartlett. Multimodal biomarkers that predict the presence of Gleason pattern 4: Potential impact for active surveillance [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr B046.
Determining Biconnectivity on a Systolic Array. (1987)

Data from 365 college students were used to assess young adults' communicative responses to older persons' painful self-disclosures (PSDs). Coupland, Coupland, and Giles (1991) proposed that recipients of PSD may respond to such disclosures via a variety of"next moves." These responses may broadly be considered to reflect forms of pro-social engagement, passive disengagement, and active disengagement. We investigated whether young adults' tendency to use certain responses to PSD were influenced by their affective reactions to PSD, their communicative background and characteristics, and the sociorelational context of the encounter in which PSD occurred. Results are discussed with respect to their implications for intergenerational interaction, and interpreted through the lens of communication accommodation theory.
Si MOS technology for spin-based quantum computing (2018)

We present recent advances made towards the realization of hole and electron spin quantum bits (qubits) localized within Si Quantum Dots (QDs). These devices, operated at cryogenic temperatures, can be defined by slightly modifying an SOI NanoWire FET fabrication flow, and are thus particularly relevant in the perspective of large-scale co-integration of qubits and their cryogenic control electronics.
A low-power mobile sensing architecture (2009)

The system and network architecture for stationary sensornets is largely solved today with many commercial solutions now available and standardization efforts underway at the IEEE, IETF, ISA, and within many industry groups. However, the existing techniques for reliable, low-power communications in stationary sensornets fail on both counts when confronted with mobility. In this dissertation, we argue that awareness of real or potential mobility enables a solution that handles the mobile case well, and supports stationary networks as a special case. This dissertation addresses micropower mobiscopes, a nascent class of mobile sensornets – small, embedded, and battery-powered systems – that experience unpredictable but structured mobility and are severely energy-constrained. We show how awareness of mobility can simplify their communication challenges, enable low-power operation, and enhance the reliability of data delivery. 
We introduce the MOV metric, a measure of mobility, and present techniques to gather it on a near nano-power budget. We also present iCount, a regulator-integrated energy meter design that allows nodes to introspect their own energy usage, and adapt their behavior to the actual energy availability and consumption. Integrating the pieces, we present three concrete hardware platforms that support our mobile sensing architecture. We develop a novel asynchronous neighbor discovery algorithm called Disco that allows nodes to operate their radios at very low duty cycles and yet still discover neighbors without any external synchronization information. Recognizing the necessity of beaconing in mobile networks, and the need for mobile-stationary node interactions, we design a link layer synchronization primitive, Backcast, and a receiver-initiated link layer, HotMac, that are suitable for mobile sensing, but also work for stationary networks across a range of conventional data collection workloads and a broad range of duty cycles. 
We evaluate our thesis with three mobile sensing applications that embody our proposed architecture. The three applications – AutoWitness, SleepTrack, and CommonSense – are representative of asset tracking, health and fitness, and participatory urban sensing, and they each stress different aspects of the architecture, including motion detection, neighbor discovery, communications, interaction patterns, energy management, and data transport. These design points illustrate that our architecture is general enough to enable a range of applications but specific enough to support them well.
Polarization-Dependent Optical Response in Anisotropic Nanoparticle-DNA Superlattices* (2020)

DNA-programmable assembly has been used to prepare superlattices composed of octahedral and spherical nanoparticles, respectively. 1386These superlattices have the same body-centered cubic lattice symmetry and macroscopic rhombic dodecahedron crystal habit but tunable lattice parameters by virtue of the DNA length, allowing one to study and determine the effect of nanoscale structure and lattice parameter on the light–matter interactions in the superlattices. Backscattering measurements and finite-difference time-domain simulations have been used to characterize these two classes of superlattices. Superlattices composed of octahedral nanoparticles exhibit polarization-dependent backscattering but via a trend that is opposite to that observed in the polarization dependence for analogous superlattices composed of spherical nanoparticles. Electrodynamic simulations show that this polarization dependence is mainly due to the anisotropy of the nanoparticles and is observed only if the octahedral nanoparticles are well-aligned within the superlattices. Both plasmonic and photonic modes are identified in such structures, both of which can be tuned by controlling the size and shape of the nanoparticle building blocks, the lattice parameters, and the overall size of the 3D superlattices (without changing habit).
ChemInform Abstract: Reactions of the Metallodrug Auranofin ((1‐Thio‐β‐D‐glucopyranose‐2,3,4,6‐tetraacetato‐S)(triethylphosphine)gold) with Biological Ligands Studied by Radioisotope Methodology. (1987)

Abstract The title compound (I) is an orally active drug in the treatment of rheumatoid arthritis.
Breast fine needle aspiration cytology practices and commonly perceived diagnostic significance of cytological features: A pan- India survey (2012)

There exist analogous as well as varied components in clinico-pathological procedures and diagnostic interpretation by individuals. These constants and variables in the practice of breast FNAC should be considered, when drawing up specifications for an assistive computational tool for analysis of breast FNAC slides. The estimate for commonly perceived significance of cytological features obtained through this study will help in their selection for computer-aided analysis of breast FNAC slides and further in selection of corresponding feature quantification techniques.
An Experimental Platform for an Indoor Location and Tracking System (2008)

In this paper, an experimental platform for indoor location and tracking using ultra wideband (UWB) impulse radio signals is presented and its performance measured. The platform has been developed entirely using standard electronic components that are commercially available. As principal goal, the experimental platform has been designed to allow a rapid performance evaluation for various system architectures and signal processing algorithms. Hence, the platform is as versatile as possible while remaining optimized for accurate location estimation. To meet these targets, the UWB receivers are implemented using a fast analog to digital converter (ADC) and a field programmable gate array (FPGA). The ADC acquires directly the received radio frequency signal. The FPGA performs the required signal processing in real time and estimates the time of arrivals (TOAs) of the received pulses. The TOAs are transferred to a personal computer (PC), where the location of the transmitter is calculated. After the description of the hardware and the algorithms, the outcomes of a measurement campaign in a laboratory environment and the accuracy of the location system are presented.
A large‐scale 19F MRI‐based cell migration assay to optimize cell therapy (2012)

Adoptive transfer of cells for therapeutic purposes requires efficient and precise delivery to the target organ whilst preserving cell function. Therefore, therapeutically applied cells need to migrate and integrate within their target tissues after delivery, e.g. dendritic cells (DCs) need to migrate to lymph nodes to elicit an antigen-specific immune response. Previous studies have shown that inappropriate cell delivery can hinder DC migration and result in insufficient immune induction. As migration can be extremely difficult to study quantitatively in vivo, we propose an in vitro assay that reproduces key in vivo conditions to optimize cell delivery and migration in vivo. Using DC migration along a chemokine gradient, we describe here a novel (19)F MR-based, large-scale, quantitative assay to measure cell migration in a three-dimensional collagen scaffold. Unlike conventional migration assays, this set-up is amenable to both large and small cell numbers, as well as opaque tissue samples and the inclusion of chemokines or other factors. We labeled primary human DCs with a (19)F label suitable for clinical use; (0.5-15) × 10(6) cells in the scaffolds were imaged sequentially, and migration was assessed using two independent methods. We found no migration with larger numbers of cells, but up to 3% with less than one million cells. Hence, we show that the cell density in cell bolus injections has a decisive impact on migration, and this may explain the limited migration observed using large cell numbers in the clinic.