gebhart/patrepeval huggingface dataset:
The Role of Genomic Data in the Discovery, Annotation and Evolutionary Interpretation of the Interferon-Lambda Family (2009)

The variable number of single exon type-I interferons in mammals, along with recently identified genes in zebrafish homologous to interferons allows a story of interferon evolution to be proposed. This model suggests that the gene duplications and single exon retrotransposons of mammalian type-III interferons are positively selected for within a genome. These characteristics are also shared with the fish interferons and could be responsible for the generation of the IL10 family and also the single exon type-I interferons.
Memory Access Optimal Algorithms for the GPU (2015)

need to consider the bank conflic of the shared
Proposed virulence-associated genes of Streptococcus suis isolates from the United States serve as predictors of pathogenicity (2021)

The proposed ofs and srtF genes were stronger predictors for differentiating pathogenic and commensal S. suis isolates compared to the classical VAGs in two sets of U.S. isolates. Pan-genome analysis in combination with metadata (serotype, ST/CC, VA genotype) was illustrated to be a valuable subtyping tool to describe the genetic diversity of S. suis.
Position estimation in induction machines utilizing rotor bar slot harmonics and carrier-frequency signal injection (2000)

This paper presents a simple and robust way of utilizing harmonic saliencies created by rotor and stator slotting, present in some induction machine designs, for the estimation of rotor position. The injection of a carrier-signal voltage, in addition to the fundamental excitation, produces a carrier-signal current that contains the desired spatial information. A closed-loop tracking observer is then used to extract this spatial information for the estimation of the rotor position. Due to its reliance on a spatial saliency and carrier-frequency signal injection, the technique is very robust over a wide speed range, including low and zero speed.
The Na-(K)-Cl cotransporter family in the mammalian kidney: molecular identification and function(s) (1996)

A new solute carrier gene family, SLC12, was recently described based on the molecular identification of three electroneutral Na-(K)-Cl cotransport proteins. In mammals, these proteins are encoded by three distinct but related genes: SLC12A1, SLC12A2, SLC12A3, which are located on different chromosomes. Although the expression patterns of these three cotransport proteins differ significantly, all of them are expressed in the mammalian kidney and participate in several important aspects of renal function. This review summarizes the information learned from the molecular identification of these cotransporters, evaluates the patterns of expression within the kidney, and discusses the roles that these cotransporters play in renal physiology and pathophysiology.
Contactless Positioning of Objects on Acoustically Reflective Surfaces by Means of Ultrasonic Forces (2022)

Ultrasonic forces have been used to keep small objects in a suspended state for a long time. In recent years, methods have been developed to manipulate the levitating objects and to lift objects located on acoustically transparent or reflective surfaces. This work demonstrates an ultrasonic levitation system, which is capable of transporting objects from and to acoustically reflective surfaces, while controlling the orientation of the levi-tating object. This requires two different types of piezoelectric transducers operating at two distinct frequencies (25 kHz and 40 kHz), a moveable reflector plate and a novel control method. With these properties, the levitation system presented in this work can be used as a precise contact-less robotic gripper for micro-manufacturing processes of small and fragile objects.
On the performance of fabricated third order laterally coupling distributed feedback 1310nm lasers (2010)

We report here on the design, fabrication and performance characteristics of 1310 nm laterally coupled distributed-feedback (LC-DFB) semiconductor lasers. We describe the epidesign of these InGaAsP/InP quantum-well ridge waveguide LC-DFB lasers, which were fabricated in a single epitaxial growth step using stepper lithography and inductively-coupled reactive-ion as well as wet chemical etching. Such a DFB fabrication process avoids the commonly required regrowth steps in conventional DFB laser fabrication processes. The lithographic tolerance has been enhanced by employing higher order gratings, yielding lasers more amenable to mass-manufacturing. In this work, uniform third-order gratings have been lithographically patterned out of the waveguide ridge built on an epitaxial structure conceived for 1310 nm lasing wavelength. We now report on L-I measurements, threshold determination and sidemode suppression ratios (SMSR) for a broad distribution of devices. These fabricated lasers achieve stable single mode lasing with SMSR as high as 54 dB under CW operation at room temperature, albeit with thresholds higher than anticipated.
Levels of Living in Rural Households (1963)

Community/Rural/Urban Development, Consumer/Household Economics
Induction of a chronic myelogenous leukemia-like syndrome in mice with v-abl and BCR/ABL. (1990)

The v-abl gene in Abelson virus induces pre-B-cell lymphoma in mice while the BCR/ABL oncogene is associated with chronic myelogenous leukemia and some cases of acute lymphocytic leukemia in humans. Understanding the mechanisms by which these oncogenes affect various cell types has been hampered by a paucity of experimental systems that reproduce the range of biological effects associated with them. We have developed an experimental system in which murine hematopoietic stem cell populations are infected with either v-abl or BCR/ABL retroviruses and are used to reconstitute lethally irradiated mice. Irrespective of the form of activated abl, greater than 90% of the animals reconstituted with such cells develop tumors. About 50% of them develop a myeloproliferative syndrome that shares several features with the chronic phase of chronic myelogenous leukemia; the remaining animals succumb to pre-B-cell lymphomas. The myeloproliferative syndrome is characterized by large numbers of clonally derived, infected myeloid cells. This model will allow study of the mechanism by which activated abl genes affect hematopoietic precursors in chronic myelogenous leukemia. Furthermore, our results demonstrate that introduction of an activated abl gene into the appropriate target cell, not the structure of the gene, is the major determinant in myeloid cell specificity.
iRoad - cooperative road infrastructure systems for driver support (2009)

The purpose of this study is to evaluate the survival of pediatric patients undergoing autologous bone marrow transplantation (auBMT) for relapsed or refractory Hodgkin lymphoma (rrHL) and to identify factors that might contribute to their outcome. We reviewed the records and clinical course of 89 consecutive rrHL patients ≤ 21 years old who underwent auBMT at Stanford Hospitals and Clinics and the Lucile Packard Children's Hospital, Stanford between 1989 and 2012. We investigated, by multiple analyses, patient, disease, and treatment characteristics associated with outcome. Endpoints were 5-year overall and event-free survival. Our findings include that cyclophosphamide, carmustine, and etoposide (CBV) as a conditioning regimen for auBMT is effective for most patients ≤ 21 years old with rrHL (5-year overall survival, 71%). Transplantation after the year 2001 was associated with significantly improved overall survival compared with our earlier experience (80% compared with 65%). Patients with multiply relapsed disease or with disease not responsive to initial therapy fared less well compared with those with response to initial therapy or after first relapse. Administration of post-auBMT consolidative radiotherapy (cRT) also appears to contribute to improved survival. We are able to conclude that high-dose chemotherapy with CBV followed by auBMT is effective for the treatment of rrHL in children and adolescents. Survival for patients who undergo auBMT for rrHL has improved significantly. This improvement may be because of patient selection and improvements in utilization of radiotherapy rather than improvements in chemotherapy. Further investigation is needed to describe the role of auBMT across the entire spectrum of patients with rrHL and to identify the most appropriate preparative regimen with or without cRT therapy in the treatment of rrHL in young patients.
Broadcast with heterogeneous node capability (2005)

In this paper, we investigate the power-efficient broadcast routing problem over heterogeneous wireless ad hoc or sensor networks where network nodes have a heterogeneous capability. The network links between pairs of nodes can no longer be modeled as symmetric or bidirectional. We show that, while most previous power-efficient algorithms work in this setting with minor modifications, they are not designed to exploit such asymmetric constraints. We present a suitable algorithm which takes into account the constraints and yet is the most power-efficient among all known algorithms.
Nonstructural Protein 2 (nsP2) of Chikungunya Virus (CHIKV) Enhances Protective Immunity Mediated by a CHIKV Envelope Protein Expressing DNA Vaccine (2013)

Chikungunya virus (CHIKV) is an important emerging mosquito-borne alphavirus, indigenous to tropical Africa and Asia. It can cause epidemic fever and acute illness characterized by fever and arthralgias. The epidemic cycle of this infection is similar to dengue and urban yellow fever viral infections. The generation of an efficient vaccine against CHIKV is necessary to prevent and/or control the disease manifestations of the infection. In this report, we studied immune response against a CHIKV-envelope DNA vaccine (pEnv) and the role of the CHIKV nonstructural gene 2 (nsP2) as an adjuvant for the induction of protective immune responses in a relevant mouse challenge model. When injected with the CHIKV pEnv alone, 70% of the immunized mice survived CHIKV challenge, whereas when co-injected with pEnv+pnsP2, 90% of the mice survived viral challenge. Mice also exhibited a delayed onset signs of illness, and a marked decrease in morbidity, suggesting a nsP2 mediated adjuvant effect. Co-injection of the pnsP2 adjuvant with pEnv also qualitatively and quantitatively increased antigen specific neutralizing antibody responses compared to vaccination with pEnv alone. In sum, these novel data imply that the addition of nsP2 to the pEnv vaccine enhances anti-CHIKV-Env immune responses and maybe useful to include in future CHIKV clinical vaccination strategies.
A 0.18-μm SiGe BiCMOS receiver and transmitter chipset for SONET OC-768 transmission systems (2003)

A 43-Gb/s receiver (Rx) and transmitter (Tx) chip set for SONET OC-768 transmission systems is reported. Both ICs are implemented in a 0.18-μm SiGe BiCMOS technology featuring 120-GHz f/sub T/ and 100 GHz f/sub max/. The Rx includes a limiting amplifier, a half-rate clock and data recovery unit, a 1:4 demultiplexer, a frequency acquisition aid, and a frequency lock detector. Input sensitivity for a bit-error rate less than 10/sup -9/ is 40 mV and jitter generation better than 230 fs rms. The IC dissipates 2.4 W from a -3.6-V supply voltage. The Tx integrates a half-rate clock multiplier unit with a 4:1 multiplexer. Measured clock jitter generation is better than 170 fs rms. The IC consumes 2.3 W from a -3.6-V supply voltage.
Supplementary Figures S7-S9 from Real-time, Near-Infrared Fluorescence Imaging with an Optimized Dye/Light Source/Camera Combination for Surgical Guidance of Prostate Cancer (2023)

&lt;p&gt;Supplementary Figures S7-S9. S7. Use of the LumiNIR{trade mark, serif} System to surgically remove a PSMA positive xenograft in a laparoscopic setting. S8. Optimization of timing and dose. S9. Kinetic quantification of YC-27 dose response.&lt;/p&gt;
Human Milk Oligosaccharides, Important Milk Bioactives for Child Health: A Perspective (2023)

Human milk contains all nutritive and bioactive compounds to give infants the best possible start in life. Human milk bioactives cover a broad range of components, including immune cells, antimicrobial proteins, microbes, and human milk oligosaccharides (HMOs). Over the last decade, HMOs have gained special attention as their industrial production has allowed the study of their structure-function relation in reductionist experimental setups. This has shed light on how HMOs steer microbiome and immune system development in early life but also how HMOs affect infant health (e.g., antibiotic use, respiratory tract infections). We are on the verge of a new era where we can examine human milk as a complex biological system. This allows not only study of the mode of action and causality of individual human milk components but also investigation of synergistic effects that might exist between different bioactives. This new wave in human milk research is largely fueled by significant advances in analytical tools in the field of systems biology and network analysis. It will be exciting to explore how human milk composition is affected by different factors, how different human milk compounds work together, and how this influences healthy infant development.
27.8 A 4600&#x03BC;m<sup>2</sup> 1.5&#x00B0;C (3&#x03C3;) 0.9kS/s thermal-diffusivity temperature sensor with VCO-based readout (2015)

Temperature sensors are widely used in microprocessors to monitor on-chip temperature gradients and hot-spots, which are known to negatively impact reliability [1-4]. Such sensors should be: 1) Small to facilitate floor planning; 2) Fast to track millisecond thermal transients and 3) Easy to trim to reduce the associated costs. Recently, it has been shown that thermal diffusivity (TD) sensors can meet these requirements [5]. TD sensors operate by digitizing the temperature-dependent delay associated with the diffusion of heat pulses through an electro-thermal filter (ETF), which, in standard CMOS, can be readily implemented as a resistive heater surrounded by a thermopile. Unlike BJT-based temperature sensors, their accuracy actually improves with CMOS scaling [6], since it is mainly limited by the accuracy of the heater/thermopile spacing, which in turn is determined by lithography. However, the readout circuitry of prior TD sensors has been based on analog phase-domain ΔΣ ADCs, which are not easily ported to low-voltage technologies, and which occupy much more area than the ETF itself [5].
Utilization of Upper Limb Joint Replacements during 1972–90: The Mayo Clinic Experience (1993)

Increasing application of expensive medical technologies, including joint replacement, is of concern in the current economic climate. Successful upper limb joint replacements (ULJRs) are being performed, but few detailed data about their utilization are available. To explore the resource implications of such surgery, the utilization of total shoulder replacement (TSR), total elbow replacement (TER) and total wrist replacement (TWR) were examined from the time these procedures first became available at the Mayo Clinic up to 1990. The age- and sex-adjusted utilization rate for TSR among Olmsted County, Minnesota, residents was 1.8 per 100,000 person-years (p-y), 0.8 per 100,000 p-y for TER and 1.1 per 100,000 p-y for TWR. Overall utilization of primary ULJR among Olmsted County residents during the 19-year study period was 3.8 per 100,000 p-y. The commonest indication for TSR was osteoarthritis (46 per cent) and for TER and TWR was rheumatoid arthritis (50 and 81 per cent respectively). There was no consistent trend in the utilization of these procedures among Olmsted County residents, but the number of referral patients receiving a ULJR at the Mayo Clinic increased steadily during the study period. The Mayo Clinic experience suggests an increasing demand for ULJR, particularly TSR and TER. With continued advances in, and diffusion of, the technology this demand may increase further.
Fabrication of engineered dopant profiles in Er/Lu:YAG transparent laser ceramics via additive manufacturing (2023)

Transparent ceramic Er:YAG laser rods were fabricated via the direct ink write (DIW) method with engineered doping profiles featuring an Er-doped core with endcaps and core-clad structures. Laser rods up to 11 cm in length were produced which required development of a scalable process. To achieve this, multiple improvements were implemented, including printing the rods horizontally on a substrate, rather than vertically, eliminating the need for an external support structure and using a sacrificial drying layer to mitigate warping and defects. Highly transparent rods were achieved with optical scatter levels as low as 0.5%/cm (at 543 nm). A small refractive index difference of 5.7 ppm was measured at the interface between the Er-doped core and the Lu-doped endcaps and cladding. These results demonstrate DIW as a straightforward method for making good optical quality laser rods with engineered doping profiles to improve laser performance.
Singlet Oxygen during Cycling of the Aprotic Sodium–O2 Battery (2017)

Aprotic sodium-O<sub>2</sub> batteries require the reversible formation/dissolution of sodium superoxide (NaO<sub>2</sub> ) on cycling. Poor cycle life has been associated with parasitic chemistry caused by the reactivity of electrolyte and electrode with NaO<sub>2</sub> , a strong nucleophile and base. Its reactivity can, however, not consistently explain the side reactions and irreversibility. Herein we show that singlet oxygen (<sup>1</sup> O<sub>2</sub> ) forms at all stages of cycling and that it is a main driver for parasitic chemistry. It was detected in- and ex-situ via a <sup>1</sup> O<sub>2</sub> trap that selectively and rapidly forms a stable adduct with <sup>1</sup> O<sub>2</sub> . The <sup>1</sup> O<sub>2</sub> formation mechanism involves proton-mediated superoxide disproportionation on discharge, rest, and charge below ca. 3.3 V, and direct electrochemical <sup>1</sup> O<sub>2</sub> evolution above ca. 3.3 V. Trace water, which is needed for high capacities also drives parasitic chemistry. Controlling the highly reactive singlet oxygen is thus crucial for achieving highly reversible cell operation.
Fluid balance modelling in patients with kidney failure (1999)

In patients with kidney failure, adequate control of fluid status remains one of the most difficult routine issues to be addressed in the modern style of dialysis. This is primarily due to the lack of quantitative methods for the assessment of fluid status and the reliance on subjective criteria. Fluid is removed from the blood during dialysis treatments using a process called ultrafiltration. The last decade has seen considerable developments in blood volume monitoring (BVM) technology which has enabled responses to ultrafiltration to be continually monitored on an individual basis. This has enabled feedback control of patients' blood volume to be applied with partial success, reducing the number of symptoms. The feedback control algorithms employed have been relatively unsophisticated, using simple proportional control with no attempt to include models of the patient fluid dynamics. This paper describes the development of some prototype fluid kinetic models which may be used in a more advanced control system. Initial results demonstrate the importance of active control processes in the patients' physiological compensatory mechanisms.
Understanding charge transport in vacuum deposited Schottky organic solar cells with microsecond transient photocurrent measurements (2014)

Schottky-junction organic solar cells have been a topic of intense research in recent times due to their surprisingly high performance. Some aspects of their device physics are well understood but charge transport in neat-C<sub>60</sub> and donor-doped Schottky junction OSCs has not been studied in detail so far. In this study, charge transport in neat-C<sub>60</sub> OSCs is examined by studying the performance of these OSCs as a function of C<sub>60</sub> active layer thickness. Surprisingly, the fillfactor of the neat-C<sub>60</sub> Schottky OSC does not degrade for layer thicknesses between 20 nm – 80 nm indicating that charge transport is not an issue. However, the short-circuit current decreases significantly due to a reduction in the builtin voltage. The dissociation of excitons formed in C<sub>60</sub> aggregates is preferentially reduced. Devices with thicker C<sub>60</sub> layers and consequently, higher C<sub>60</sub> aggregation, were found to have greater recombination. Finally, charge mobility in C<sub>60</sub> films with aggregates is found to be lower than charge mobility in films with little to no aggregation.
Trajectory-based triggering system for hyperspectral imaging flow cytometer (2023)

A hyperspectral imaging flow cytometer can acquire high-resolution hyperspectral images of particles, such as biological cells, flowing through a microfluidic system. A trajectory-based triggering system can be used that will only trigger the acquisition of a hyperspectral image when an appropriate particle or cell is crossing an imaging line, thereby saving valuable resources and time. The hyperspectral imaging flow cytometer can provide detailed spatial maps of multiple emitting species, cell morphology information, and state of health. An optimized system can image about 20 cells per second. The hyperspectral imaging flow cytometer enables many thousands of cells to be characterized in a single session.
Structural and thermoelectric properties of CH3NH3SnI3 perovskites processed by applying high pressure with shear strain (2022)

CH3NH3SnI3 perovskites, which can be created using printing technology, are environmentally friendly thermoelectric materials, but their applications are limited by unsatisfactory thermoelectric efficiency and structural stability. In this work, CH3NH3SnI3 perovskites are processed by applying high pressure with shear strain for the first time, resulting in better structural stability, enhanced electrical conductivity and the Seebeck coefficient with CH3NH3SnI3 tube structures after processing. First-principles calculations verified the reasonable changes in lattice constants, electronic band structures, electrical conductivity and the Seebeck coefficient. The present study demonstrates a potential strategy to improve the structural and thermoelectric properties of CH3NH3SnI3 and uncovers the possible mechanism.
Supplementary Data from Acquired Resistance to Combination Treatment with Temozolomide and ABT-888 Is Mediated by Both Base Excision Repair and Homologous Recombination DNA Repair Pathways (2023)

Supplementary Data from Acquired Resistance to Combination Treatment with Temozolomide and ABT-888 Is Mediated by Both Base Excision Repair and Homologous Recombination DNA Repair Pathways
Integration of Melting Excimer Laser Annealing in Power MOS Technology (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> The integration of excimer laser annealing (ELA) into the power MOS device technology has been studied and evaluated. The integration issues include patterning effect, extreme nonequilibrium kinetics of dopant and defects, material modification due to the melting-regrowth phenomena (in the melting regime), and residual implant damage. We demonstrated that ELA can be applied as a reliable, effective, and advantageous process in the context of semiconductor device fabrication. In particular, power MOS field-effect transistors were successfully fabricated with superior electrical characteristics than those fabricated according to the standard process. Optimization of the process was achieved through extensive characterization analyses, while an intense research effort was dedicated to the development of a technology computer-aided design tool for the simulation of the laser annealing process in Si-based devices. The electrical characterization of the transistor fabricated by ELA is presented, showing a device yield of 90% on wafer. </para>