gebhart/patrepeval huggingface dataset:
Investigation of Hematopoietic Stem Cell and Progenitor Populations: Implication for Cell Fate Determination and Lineage Commitment. (2005)

Abstract A thorough understanding of the lineage potential of each subset of hematopoietic stem cells (HSC) and progenitor populations is critical to establish an accurate map of cell fate determination during hematopoietic development. A controversy exists whether multipotentiality is conserved until a mutually exclusive segregation of myeloid and lymphoid potentials or whether early progenitor populations sequentially lose lineage potential as they differentiate from the long-term self-renewing HSC (LT-HSC), starting with loss of megakaryocyte/erythrocyte (MegE) potential. Hematopoietic cells at different developmental stages can be prospectively isolated based on a combination of cell surface phenotypes and functional assays in vitro and in vivo. However, assessment of lineage potential of cells other than LT-HSC is complicated by the progressive loss of self-renewal activity in progenitor populations and the lack of congenic surface markers on mature cells of the MegE lineage. Using sensitive in vitro and in vivo approaches, we quantitatively and kinetically assessed the MegE potential of Lineage−/c-Kit+/Sca-1+ (KLS) subsets of mouse bone marrow, including LT-HSC (Thy1.1int/Flk-2−), sort-term HSC (ST-HSCF: Thy1.1int/Flk-2+) and multipotent progenitor population (MPPF: Thy1.1−/Flk-2+), and compared it with the MegE potential of downstream myeloid progenitors (CMP, GMP and MEP) and with their ability to give rise to mature myelomonocytic and lymphoid cells. In contrast to previous reports, we demonstrate that Flk2-positive ST-HSCF and MPPF populations have readily detectable but transient MegE potential in vivo that is more robust than committed myeloid progenitors CMP and MEP. We also show that these cells make clonal colonies in vitro and in vivo in the spleen that contained megakaryocytes and erythrocytes. Moreover, we established the kinetics of mature cell production from each stem and progenitor population, hence providing the timing of these early differentiation events in vivo that is of critical importance when investigating lineage potential. Our results demonstrate that multipotentiality is retained in the KLS “stem cell” fraction of the bone marrow and support a model of hematopoietic development with mutually exclusive segregation of myeloid and lymphoid lineage potential. Taken together with previous findings, they indicate that transition from LT-HSC to ST-HSCF and then to MPPF, is accompanied by progressive lose of self-renewal ability, increased proliferation and change in gene expression programs to prepare multipotent cells to leave the stem cell niche and undergo lineage differentiation. This model is by definition a simplification of a complex biological process but accounts for most, if not all, differentiation events, tolerates plasticity in lineage segregation at early steps of commitment and it accommodates intrinsic lineage preferences during ontogeny and aging.
Interactively skimming recorded speech (1994)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Program in Media Arts & Sciences, 1994.
Inhibition of the PI3K Pathway by T-DM1 and its Maytansinoid-Conjugate (2016)

Raoof, Mustafa MD; Yuan, Yuan MD, PhD; Wen, Wei; Yan, Jin; Xing, Quanhua; Han, Ernest; Yim, John H. MD, FACS Author Information
The flexcode source-channel coding approach for audio and speech transmission (2010)

The FlexCode project is a joint research project of KTH Stockholm, RWTH
Elevated liver iron concentration is a marker of increased morbidity in patients with thalassemia intermedia (2011)

Elevated liver iron concentration in patients with β thalassemia intermedia is a marker of increased vascular, endocrine, and bone disease.
Reduced-intensity conditioning followed by allografting of hematopoietic cells can produce clinical and molecular remissions in patients with poor-risk hematologic malignancies (2002)

A reduced-intensity conditioning regimen was investigated in 45 patients with hematologic malignancies who were considered poor candidates for conventional myeloablative regimens. Median patient age was 49 years. Twenty-six patients previously failed autologous transplantation, and 18 patients had a refractory disease at the time of transplantation. In order to decrease nonrelapse mortality, and enhance the graft-versus-tumor effect, a program was designed in which a reduced conditioning with thiotepa, fludarabine, and cyclophosphamide was associated with programmed reinfusions of donor lymphocytes for patients without graft-versus-host disease (GVHD), not achieving clinical and molecular remission after transplantation. GVHD prophylaxis consisted of cyclosporine A and methotrexate. Seventeen patients received marrow cells and 28 received mobilized hematopoietic cells. All patients engrafted. The probability of grades II-IV and III-IV acute GVHD were 47% and 13%, respectively. The probability of nonrelapse mortality, progression-free survival, and overall survival were 13%, 57%, and 53%, respectively. Thirteen patients in complete remission had a polymerase chain reaction marker for minimal disease monitoring; 10 achieved molecular remission after transplantation. Nine patients received donor lymphocytes: one patient with mantle cell lymphoma had a minimal response, one patient with refractory anemia with excess of blasts in transformation achieved complete remission, and 7 patients did not respond. At a median follow-up of 385 days (range, 24 to 820 days), 25 patients (55%) were alive in complete remission. Although longer follow-up is needed to evaluate the long-term outcome, the study shows that this regimen is associated with a durable engraftment, has a low nonrelapse mortality rate, and can induce clinical and molecular remissions.
CELLULAR PATHWAYS FOR REJECTION OF CLASS-I-MHCDISPARATE SKIN AND TUMOR ALLOGRAFTS1 (1988)

We have investigated the relative roles of the Lyt-2+ and L3T4+ T lymphocyte subsets in rejection of class-I-MHC-antigen-disparate skin and tumor allografts. To deplete T cells in vivo, rat anti-Lyt-2 or anti-L3T4 monoclonal antibodies (mAb) were administered to adult-thymectomized (ATX) recipient mice prior to transplantation. BALB/c (H-2d) recipient mice rejected the Ia- Sarcoma I (Sa1) (H-2a) tissue culture-derived tumor after depletion of the L3T4+ T cell subset in vivo. In contrast, depletion of the Lyt-2+ T cell subset permitted lethal tumor growth in all recipient mice. To determine the role of particular T cell subsets in rejection of Ld class-I-MHC-antigen-disparate allografts, BALB/c skin was transplanted to BALB/c-H-2dm2 recipient mice. Skin grafts were rejected by control mice with a mean survival time (MST) of 14.5 days. The MST of skin grafts for mice treated with anti-L3T4 mAb was 16.6 days. In contrast, administration of anti-Lyt-2 mAb alone (MST = greater than 47 days) or together with anti-L3T4 mAb (MST = greater than 50 days) caused prolonged or indefinite graft survival in all recipient mice. Depletion of specific T cell subsets was confirmed by flow cytometric analysis and by analysis of T cell function in vitro. These results suggest that Lyt-2+ T lymphocytes are essential for rejection of class-I-MHC-disparate allografts; indirect presentation of alloantigen to L3T4+ T cells may not be necessary for rejection.
pX STANDARDS (2018)

The distance of closest approach parameter in the Debye-Huckel theory is greater than the sum of the crystallographic radii for most salts, often by about the radius of a water molecule for each ion. This suggests that it should be the sum of the hydrated radii, that is, that the mean rational activity coefficient predicted by the Debye-Huckel theory is that of the hydrated ions. In calculating the molality, one does not usually take into account that some of the solvent is associated with the solute. However, the chemical potential of the solute will be different from its value if the solute is consid- ered unhydrated. The total free energy of the system is the same, regardless of the way it is considered broken down; hence, this fact can be used to find the relationship between the activity coefficients.
The Low M r Protein-tyrosine Phosphatase Is Involved in Rho-mediated Cytoskeleton Rearrangement after Integrin and Platelet-derived Growth Factor Stimulation (2000)

The low molecular weight protein-tyrosine phosphatase (LMW-PTP) is an enzyme that is involved in the early events of platelet-derived growth factor (PDGF) receptor signal transduction. In fact, LMW-PTP is able to specifically bind and dephosphorylate activated PDGF receptor, thus modulating PDGF-induced mitogenesis. In particular, LMW-PTP is involved in pathways that regulate the transcription of the immediately early genes myc and fos in response to growth factor stimulation. Recently, we have found that LMW-PTP exists constitutively in cytosolic and cytoskeleton-associated localization and that, after PDGF stimulation, c-Src is able to bind and phosphorylate LMW-PTP only in the cytoskeleton-associated fraction. As a consequence of its phosphorylation, LMW-PTP increases its catalytic activity about 20-fold. In this study, our interest was to investigate the role of LMW-PTP phosphorylation in cellular response to PDGF stimulation. To address this issue, we have transfected in NIH-3T3 cells a mutant form of LMW-PTP in which the c-Src phosphorylation sites (Tyr(131) and Tyr(132)) were mutated to alanine. We have established that LMW-PTP phosphorylation by c-Src after PDGF treatment strongly influences both cell adhesion and migration. In addition, we have discovered a new LMW-PTP substrate localized in the cytoskeleton that becomes tyrosine-phosphorylated after PDGF treatment: p190Rho-GAP. Hence, LMW-PTP plays multiple roles in PDGF receptor-mediated mitogenesis, since it can bind and dephosphorylate PDGF receptor, and, at the same time, the cytoskeleton-associated LMW-PTP, through the regulation of the p190Rho-GAP phosphorylation state, controls the cytoskeleton rearrangement in response to PDGF stimulation.
Generative Adversarial Perturbations (2018)

In this paper, we propose novel generative models for creating adversarial examples, slightly perturbed images resembling natural images but maliciously crafted to fool pre-trained models. We present trainable deep neural networks for transforming images to adversarial perturbations. Our proposed models can produce image-agnostic and image-dependent perturbations for both targeted and non-targeted attacks. We also demonstrate that similar architectures can achieve impressive results in fooling classification and semantic segmentation models, obviating the need for hand-crafting attack methods for each task. Using extensive experiments on challenging high-resolution datasets such as ImageNet and Cityscapes, we show that our perturbations achieve high fooling rates with small perturbation norms. Moreover, our attacks are considerably faster than current iterative methods at inference time.
Accelerated Phase of Myeloproliferative Neoplasms (2021)

MPN-AP/BP has a markedly different mutational profile from de novo acute myeloid leukemia (AML). In MPN-AP/BP, TP53 and IDH1/2 are more frequent, whereas FLT3 and DNMT3A are rare. Higher incidence of leukemic transformation has been associated with the most aggressive MPN subtype, myelofibrosis (MF); other risk factors for leukemic transformation include rising blast counts above 3-5%, advanced age, severe anemia, thrombocytopenia, leukocytosis, increasing bone marrow fibrosis, type 1 CALR-unmutated status, lack of driver mutations (negative for JAK2, CALR, or MPL genes), adverse cytogenetics, and acquisition of ≥2 high-molecular risk mutations (ASXL1, EZH2, IDH1/2, SRSF2, and U2AF1Q157). The aforementioned factors have been incorporated in several novel prognostic scoring systems for MF. Currently, elderly/unfit patients with MPN-AP/BP are treated with hypomethylating agents with/without ruxolitinib; these regimens appear to confer comparable benefit to intensive chemotherapy but with lower toxicity. Retrospective studies in patients who acquired actionable mutations during MPN-AP/BP showed positive outcomes with targeted AML treatments, such as IDH1/2 inhibitors, and require further evaluation in clinical trials. Key Messages: Therapy for MPN-AP patients represents an unmet medical need. MF patients, in particular, should be appropriately stratified regarding their prognosis and the risk for transformation. Higher-risk patients should be monitored regularly and treated prior to progression to MPN-BP. MPN-AP patients may be treated with hypomethylating agents alone or in combination with ruxolitinib; also, patients can be provided with the option to enroll in rationally designed clinical trials exploring combination regimens, including novel targeted drugs, with an ultimate goal to transition to transplant.
10 K Ring Electrode Trap—Tandem Mass Spectrometer for Infrared Spectroscopy of Mass Selected Ions (2009)

A novel instrumental setup for measuring infrared photodissociation spectra of buffer gas cooled, mass‐selected ions is described and tested. It combines a cryogenically cooled, linear radio frequency ion trap with a tandem mass spectrometer, optimally coupling continuous ion sources to pulsed laser experiments. The use of six independently adjustable DC potentials superimposed over the trapping radio frequency field provides control over the ion distribution within, as well as the kinetic energy distribution of the ions extracted from the ion trap. The scheme allows focusing the ions in space and time, such that they can be optimally irradiated by a pulsed, widely tunable infrared photodissociation laser. Ion intensities are monitored with a time‐of‐flight mass spectrometer mounted orthogonally to the ion trap axis.
Immunohistochemical analysis of a cerebral arteriovenous malformation obliterated by radiosurgery and presenting with re-bleeding. Case report (2003)

The purpose of this study was to analyze immunohistochemical characteristics of the cell population in a radiosurgically obliterated cerebral arteriovenous malformation (AVM) after recurrent hemorrhage. Immunohistochemical reactions were carried out on paraffin-embedded histological sections for von Willebrand factor (FVIII), CD34 endothelial antigen (CD34), vimentin and alpha-smooth-muscle actin (SMA) cytoskeletal proteins. Histopathological analysis revealed that the majority of AVM channels were replaced by hypocellular scar tissue. However some of them still disclosed thrombus organization by granulation tissue seven years after radiosurgery. FVIII and CD34 reactions revealed vessel neoformation in thromboses. Proliferating spindle-shaped cells with SMA and vimentin expression were identified in the granulation tissue. These histopathological findings suggest the role of re-canalization in recurrence of hemorrhage following radiosurgical obliteration of the AVM. Contribution of myofibroblastic elements in the vessels' occlusion after radiosurgery is also demonstrated.
Flow cytometric sorting of frozen–thawed spermatozoa in sheep and non-human primates (2004)

Research was conducted in sheep to determine an effective preparation method for high-purity sorting of frozen-thawed spermatozoa. The efficacy of sorting frozen-thawed spermatozoa was then investigated in several non-human primate species. An aliquot of each ejaculate (three rams, three ejaculates per ram) was processed as a fresh control (FRESH). Frozen spermatozoa were thawed and prepared for sorting by no further processing (FT-NEAT), washing (FT-WASH) or gradient centrifugation (FT-GRADIENT) and evaluated for motility at 1 h post-staining and motility and acrosomal status at 0 and 4 h post-sorting. Samples were analysed using a high-speed cell sorter. High levels of purity for X- and Y-enriched samples were achieved for all treatments (85-92%). The percentage of motile spermatozoa before sorting was lower (P < 0.05) for frozen-thawed samples (FT-NEAT: 32.7 +/- 2.5%; FT-WASH: 32.2 +/- 3.3%; FT-GRADIENT: 73.9 +/- 3.7%) compared with FRESH (83.3 +/- 1.2%). Post-sorting, the percentage of motile spermatozoa before and after incubation for FT-NEAT (60.0 +/- 5.1% and 27.2 +/- 6.1% for 0 and 4 h, respectively) was lower than that for FRESH (87.8 +/- 0.9% and 83.3 +/- 1.2% for 0 and 4 h, respectively; P < 0.05), FT-WASH (80.0 +/- 2.4% and 71.7 +/- 3.6% for 0 and 4 h, respectively; P < 0.05) and FT-GRADIENT (84.4 +/- 1.3% and 77.2 +/- 1.7% for 0 and 4 h, respectively; P < 0.05). Vanguard sperm migration distance through artificial cervical mucus was lower (P < 0.05) for FT-NEAT (17.7 +/- 1.7 mm) compared with FT-WASH (29.1 +/- 3.8 mm) and FT-GRADIENT (28.4 +/- 2.0 mm) and similar (P < 0.05) to FRESH (23.7 +/- 1.8 mm). Sample preparation using a modified wash method enabled high-purity sorting (range 86-97% purity) of frozen-thawed epididymal spermatozoa in the baboon (Papio hamadryas), common marmoset (Callithrix jacchus) and common chimpanzee (Pan troglodytes). For all non-human primate species, sorted spermatozoa were progressively motile (marmoset: 20.5 +/- 5.5%; baboon: 37.5 +/- 2.5%; chimpanzee: 73.0 +/- 2.0%), acrosome intact (marmoset: 68.5 +/- 7.5%; baboon: 89.5 +/- 1.5%; chimpanzee: 84.0 +/- 1.0%) and able to penetrate an artificial cervical mucus. In summary, high-purity sorting of frozen-thawed ram and non-human primate spermatozoa with recovery of progressively motile, acrosome-intact spermatozoa was possible after processing to remove cryodiluent.
Diabetes, Sports and Exercise (2020)

Contractions of the peripheral skeletal muscles increase muscular energy consumption.
First Borehole Acoustic Reflection Survey mapping a deepwater turbidite sand (2006)

The South Marlim oil field, discovered in 1987 offshore Campos Basin, Brazil, saw in the 1990's some deepwater production records being established and the development plans for the field should allow reaching a peak production of 420,000 boe/d in 2010. South Marlim is a turbidite reservoir of Upper Oligocene‐Lower Miocene age. These reservoirs were initially thought to be homogeneous, widespread turbidite fans, but more recent studies based on later well data and 3D seismic surveys found that they can be rather complex and heterogeneous (Bruhn, 2001). In order to better define the turbidite reservoir geometry at one South Marlim's horizontal producer location, Petrobras decided to run a Borehole Acoustic Reflection Survey (BARS), the first time ever this was attempted in this type of environment. The Sonic Scanner™ tool from Schlumberger was drill‐pipe conveyed (TLC) in order to collect the data. The processed images have a depth of investigation of 10 m and a vertical resolution of 0.3 m. The BARS technique mapped the main turbidite sand over 544m of horizontal well section, showing thickness variations between 4 and 10m. No other measurement provided this level of information. At the pilot‐hole, the sand was 4 meter thick and the horizontal well was geosteered assuming constant sand thickness. A flat spot event was mapped one meter above the tip of the well, suggesting segregated gas in that reservoir area, which lies on a structural high. The well produced limited amounts of gas supporting the direct gas‐oil contact indicator from the acoustic method. This is possibly the first fluid contact ever mapped by deep sonic imaging technique. The BARS images were consistent with the dips estimated from image logs, with the geosteering data and to a great extent, with the pilot‐hole results. Their correlation with surface seismic is encouraging, despite the enormous scale differences. Petrobras plans to use the high‐resolution sonic images in order to provide lateral constraints to seismic acoustic impedance inversion and as an input to geological modeling. The resulting improvements in the static model should in turn enhance considerably the prediction capability of the reservoir dynamics simulators.
Tuple Packing: Efficient Batching of Small Graphs in Graph Neural Networks (2022)

When processing a batch of graphs in machine learning models such as Graph Neural Networks (GNN), it is common to combine several small graphs into one overall graph to accelerate processing and remove or reduce the overhead of padding. This is for example supported in the PyG library. However, the sizes of small graphs can vary substantially with respect to the number of nodes and edges, and hence the size of the combined graph can still vary considerably, especially for small batch sizes. Therefore, the costs of excessive padding and wasted compute are still incurred when working with static shapes, which are preferred for maximum acceleration. This paper proposes a new hardware agnostic approach -- tuple packing -- for generating batches that cause minimal overhead. The algorithm extends recently introduced sequence packing approaches to work on the 2D tuples of (|nodes|, |edges|). A monotone heuristic is applied to the 2D histogram of tuple values to define a priority for packing histogram bins together with the objective to reach a limit on the number of nodes as well as the number of edges. Experiments verify the effectiveness of the algorithm on multiple datasets.
Design Issues for Graphical Unix User Interfaces (1990)

This paper discusses important usability issues that impact the future development of graphical user interfaces for UNIX. UNIX provides a user with the capability to combine basic commands using input/output redirection to create new commands to perform more complex tasks. The new graphical interfaces do not directly aid composing commands. However, it takes more than five years of experience to begin to be able to fluently compose new, complex commands. This paper describes a methodology which focuses attention on the problems that must be solved in order for these core features of UNIX to be accessible to individuals with one to five years of experience.
Manifold signal receiver for powerline communication systems (2011)

Amalgamation of multiple signal transmission through a singular medium is the paramount advantage offered in the Powerline Communications (PLC) architecture. We propose a PLC paradigm, which allows for one receiver to control all types of signals, effectively delineating a universal communication system. Firstly, when different types of signals are received on power lines the receiver needs intelligent channel estimation for decoupling these signals. An intelligent blind channel estimation scheme is proposed for achieving this. Secondly the received signals (telephone, broadband, radio, television etc.,) need to be classified and routed to the appropriate devices. To accomplish this we propose a novel optimized coulomb energy neural network (OCENN) for classification of incoming signals. Experimental results over real time PLC low voltage system shows that the Universal Powerline Receiver (UPR) achieves a throughput of 75 mbps, 63 mbps and 56 mbps at SNR of 30 dB for the data, telephone and television transmissions respectively. Comparative analysis of UPR with existing state of art OFDM and FMT modems is presented, which shows UPR as a viable prospective option.
Cluster of Norovirus Genogroup IX Outbreaks in Long-Term Care Facilities, Utah, USA, 2021 (2022)

We report 5 clustered acute gastroenteritis outbreaks in long-term care facilities in Utah, USA, that were linked to healthcare employees working at multiple facilities. Four outbreaks were caused by norovirus genotype GIX. We recommend continued norovirus surveillance and genotyping to determine contributions of this genotype to norovirus outbreaks.
A Perfectly Hydrophobic Surface (θA/θR = 180°/180°) (2006)

A perfectly hydrophobic surface with both advancing and receding water contact angles of 180 degrees was prepared using a facile method on a silicon wafer. Phase separation of a toluene-swollen covalently attached methylsilicone results in a nanoscale network structure that is responsible for the superhydrophobicity. A method for testing extreme hydrophobicity was devised to distinguish between surfaces exhibiting contact angles of 180 and 179 degrees .