gebhart/patrepeval huggingface dataset:
The effect of incomplete knowledge on the diagnoses of a computer consultant system (1991)

The knowledge bases (KBs) of diagnostic decision support systems are often incomplete, and gaps in the KB could potentially lead systems to reach diagnoses that are implausible to physicians. To investigate this possibility we studied Iliad (Version 2.01), a computer consultant system that generates differential diagnosis across the domain of internal medicine. Data from the history, physical examination, and laboratory findings of 50 grand-rounds cases were entered into Iliad by a computer consultant aware of the diagnosis but blinded to its presence or absence in Iliad's KB. Two experienced internists were asked to diagnose these cases before and after seeing the results of the computer consultation, and to assess the plausibility of the computer's diagnoses. Twenty-eight of the 50 cases (56.0%) were diseases contained in Iliad's KB. After seeing Iliad's diagnoses for cases in the KB, physicians assigned to their correct diagnoses a higher mean ranked position (1.5 versus 2.0, p less than 0.008) and a higher mean probability (84.0% versus 77.6%, p less than 0.008) compared with their pre-Iliad values, whereas for cases not in the KB, mean position and probability for correct diagnoses did not change. Physician diagnostic accuracy did not change after consultation on cases included or not included in the KB. After adjusting for case difficulty, mean plausibility of Iliad's diagnoses was judged significantly higher (on a seven-point scale) for cases in the KB than for cases not in the KB (4.2 versus 3.2, p less than 0.02).(ABSTRACT TRUNCATED AT 250 WORDS)
Continuum Robots for Medical Applications: A Survey (2015)

In this paper, we describe the state of the art in continuum robot manipulators and systems intended for application to interventional medicine. Inspired by biological trunks, tentacles, and snakes, continuum robot designs can traverse confined spaces, manipulate objects in complex environments, and conform to curvilinear paths in space. In addition, many designs offer inherent structural compliance and ease of miniaturization. After decades of pioneering research, a host of designs have now been investigated and have demonstrated capabilities beyond the scope of conventional rigid-link robots. Recently, we have seen increasing efforts aimed at leveraging these qualities to improve the frontiers of minimally invasive surgical interventions. Several concepts have now been commercialized, which are inspiring and enabling a current paradigm shift in surgical approaches toward flexible access routes, e.g., through natural orifices such as the nose. In this paper, we provide an overview of the current state of this field from the perspectives of both robotics science and medical applications. We discuss relevant research in design, modeling, control, and sensing for continuum manipulators, and we highlight how this work is being used to build robotic systems for specific surgical procedures. We provide perspective for the future by discussing current limitations, open questions, and challenges.
Excess information at bacteriophage T7 genomic promoters detected by a random cloning technique (1989)

In our previous analysis of the information at binding sites on nucleic acids, we found that most of the sites examined contain the amount of information expected from their frequency in the genome. The sequences at bacteriophage T7 promoters are an exception, because they are far more conserved (35 bits of information content) than should be necessary to distinguish them from the background of the Escherichia coli genome (17 bits). To determine the information actually used by the T7 RNA polymerase, promoters were chemically synthesized with many variations and those that function well in an in vivo assay were sequenced. Our analysis shows that the polymerase uses 18 bits of information, so the sequences at phage genomic promoters have significantly more information than the polymerase needs. The excess may represent the binding site of another protein.
Comparative Evaluation of Immunochemical Fecal Occult Blood Tests for Colorectal Adenoma Detection (2009)

The German Research Foundation (Deutsche Forschungsgemeinschaft) within the framework of a PhD program (Graduiertenkolleg 793).
Acquired immunodeficiency syndrome-associated non-Hodgkin's lymphomas and other malignancies in patients with hemophilia (1993)

Non-Hodgkin's lymphoma (NHL) is the most common human immunodeficiency virus (HIV)-associated malignancy in hemophiliacs. We studied the incidence and clinicopathologic features of NHL in 3,041 hemophiliacs followed at 18 US Hemophilia Centers between 1978 and 1989. Of the 1,295 (56.6%) who were HIV(+), 253 (19.5%) developed acquired immunodeficiency syndrome (AIDS), of whom 14 (5.5%) developed NHL. Three NHL occurred in HIV(-) hemophiliacs, for a 36.5-fold greater risk in HIV(+) than HIV(-) hemophiliacs (P < .001). The NHL incidence rate was 29-fold greater than in the US population by Surveillance, Epidemiology, and End Results (SEER) estimates (P < .001). Between 0 and 4 lymphomas have been observed per year between 1978 and 1989. At presentation 13 (92.9%) of the HIV(+) NHL were extranodal. Ten were stage IV, 1 stage II, and 3 stage IE. Ten (71.4%) were high-grade, 3 (21.4%) intermediate-grade, and 1 (7.1%) was a low-grade B-cell lymphoma. Epstein-Barr virus (EBV) DNA was detected in 36% by in situ hybridization, including one central nervous system (CNS) lymphoma. The mean CD4 cell count at NHL diagnosis was 64/mm3, the mean latency from initial HIV infection was estimated to be 59 months, and the median survival was 7 months. The incidence of basal cell carcinoma in HIV(+) hemophiliacs was 18.3-fold greater than in HIV(-) hemophiliacs (P < .001) and 11.4-fold greater than in the US population (P < .001). In conclusion, incidence rates of NHL and basal cell carcinoma in HIV(+) hemophiliacs are significantly increased over rates in HIV(-) hemophiliacs and over rates in the US population. Clinicopathologic presentation of NHL in HIV(+) hemophiliacs is similar to that in HIV(+) homosexual men.
A phase II trial of erlotinib in patients with recurrent malignant gliomas and nonprogressive glioblastoma multiforme postradiation therapy (2009)

Patients with (a) recurrent malignant glioma (MG): glioblastoma (GBM) or recurrent anaplastic glioma (AG), and (b) nonprogressive (NP) GBM following radiation therapy (RT) were eligible. Primary objective for recurrent MG was progression-free survival at 6 months (PFS-6) and overall survival at 12 months for NP GBM post-RT. Secondary objectives for recurrent MGs were response, survival, assessment of toxicity, and pharmacokinetics (PKs). Treatment with enzyme-inducing antiepileptic drugs was not allowed. Patients received 150 mg/day erlotinib. Patients requiring surgery were treated 7 days prior to tumor removal for PK analysis and effects of erlotinib on epidermal growth factor receptor (EGFR) and intracellular signaling pathways. Ninety-six patients were evaluable (53 recurrent MG and 43 NP GBM); 5 patients were not evaluable for response. PFS-6 in recurrent GBM was 3% with a median PFS of 2 months; PFS-6 in recurrent AG was 27% with a median PFS of 2 months. Twelve-month survival was 57% in NP GBMs post-RT. Primary toxicity was dermatologic. The tissue-to-plasma ratio normalized to nanograms per gram dry weight for erlotinib and OSI-420 ranged from 25% to 44% and 30% to 59%, respectively, for pretreated surgical patients. No effect on EGFR or intratumoral signaling was seen. Patients with NP GBM post-RT who developed rash in cycle 1 had improved survival (P < .001). Single-agent activity of erlotinib is minimal for recurrent MGs and marginally beneficial following RT for NP GBM patients. Development of rash in cycle 1 correlates with survival in patients with NP GBM after RT.
Liquid Metal–Elastomer Soft Composites with Independently Controllable and Highly Tunable Droplet Size and Volume Loading (2019)

Soft composites are critical for soft and flexible materials in energy harvesting, actuators, and multifunctional devices. One emerging approach to create multifunctional composites is through the incorporation of liquid metal (LM) droplets such as eutectic gallium indium (EGaIn) in highly deformable elastomers. The microstructure of such systems is critical to their performance; however, current materials lack control of particle size at diverse volume loadings. Here, we present a fabrication approach to create liquid metal-elastomer composites with independently controllable and highly tunable droplet size (100 nm ≤ D ≤ 80 μm) and volume loading (0 ≤ ϕ ≤ 80%). This is achieved through a combination of shear mixing and sonication of concentrated LM/elastomer emulsions to control droplet size and subsequent dilution and homogenization to tune LM volume loading. These materials are characterized utilizing dielectric spectroscopy supported by analytical modeling, which shows a high relative permittivity of 60 (16× the unfilled elastomer) in a composite with ϕ = 80%, a low tan δ of 0.02, and a significant dependence on ϕ and minor dependence on droplet size. Temperature response and stability are determined using dielectric spectroscopy through temperature and frequency sweeps with DSC. These results demonstrate a wide temperature stability of the liquid metal phase (crystallizing at <-85 °C for D < 20 μm). Additionally, all composites are electrically insulating across wide frequency (0.1 Hz-10 MHz) and temperature (-70 to 100 °C) ranges even up to ϕ = 80%. We highlight the benefit of LM microstructure control by creating all-soft-matter stretchable capacitive sensors with tunable sensitivity. These sensors are further integrated into a wearable sensing glove where we identify different objects during grasping motions. This work enables programmable LM composites for soft robotics and stretchable electronics where flexibility and tunable functional response are critical.
Bisecting N-acetylglucosamine on K562 cells suppresses natural killer cytotoxicity and promotes spleen colonization. (1996)

beta 1-4 N-acetylglucosaminyltransferase (GnT-III) catalyzes the formation of bisecting N-acetylglucosamine (GlcNAc) in the biosynthesis of N-linked oligosaccharides. To examine the effect of bisecting GlcNAc on the natural killer (NK) cytotoxicity, the GnT-111 gene was introduced into NK-sensitive K562 cells that have no detectable GnT-III activity. We obtained three clones stably expressing high GnT-III (positive transfectants). Introduction of the GnT-III gene resulted in an increase of bisecting GlcNAc and a decrease of external sialic acid as well as tri- and tetraantennary sugars, as judged by flow cytometry. Compared to controls, the NK cytotoxicity was completely blocked against positive transfectants. The binding of effector cells to positive transfectants was also decreased. After s.c. injection into nude mice, positive transfectants produced spleen colonization, although no spleen lesions were formed by control cells. In nude mice depleted of NK cells by anti-asialo GM1 antibody, both positive transfectants and controls produced spleen colonization equally. These results indicate that K562 cells expressing GnT-III are resistant to NK cytotoxicity, resulting in spleen colonization in nude mice.
Survival in Recipients of Marginal Cadaveric Donor Kidneys Compared with Other Recipients and Wait-Listed Transplant Candidates (2001)

An increasing number of cadaveric kidney transplants are now performed with organs from donors who would have been deemed unsuitable in earlier times. Although good allograft outcomes have been obtained with these marginal donor transplants, it is unclear whether recipients of marginal kidney transplants achieve a reduction in long-term mortality as do recipients of "ideal" kidneys. Patients with end-stage renal disease registered on the cadaveric renal transplant waiting list between January 1, 1992, and June 30, 1997, were studied for mortality risks according to three outcomes: wait-listed on dialysis treatment with no transplant (WLD); transplantation with marginal donor kidney (MDK); and "ideal" or optimal donor kidney transplantation (IDK). Thirty-four percent of wait-list registrants had received a cadaveric kidney transplant by June 30, 1998. Of these, 18% received a marginal kidney that had one or more of the following pretransplant factors: donor age >55 yr, non-heartbeating donor, cold ischemia time >36 h, and donor hypertension or diabetes mellitus of > 10 yr duration. Five-year graft and patient survival was 53% and 74% for MDK recipients compared with 67% (P< 0.001) and 80% (P< 0.001) for IDK recipients. Adjusted annual death rate and estimated remaining life time was 6.3%, 4.7%, and 3.3% and 15.3 yr, 20.4 yr, and 28.7 yr for WLD, MDK, and IDK groups, respectively. The average increase in life expectancy for MDK recipients compared with the WLD cohort was 5 yr, although this benefit varied from 3 to 10 yr depending on the recipient's characteristics. It is concluded that transplantation of a marginal kidney is associated with a significant survival benefit when compared with maintenance dialysis.
Abortive transformation of temperature‐sensitive mutants of rat 3Y1 cells by simian virus 40: Effect of cellular arrest states on entry into S phase and cellular proliferation (1985)

Four temperature-sensitive (ts) mutants of rat 3Y1 fibroblasts, representing independent complementation groups, cease to proliferate predominantly with a 2n DNA content, at the restrictive temperature (39.8 degrees C) (temperature arrest) or at the permissive temperature (33.8 degrees C) at a confluent cell density (density arrest) (Ohno et al., 1984). We studied the temperature- or the density-arrested cells of these mutants infected with simian virus 40 (SV40) or its mutants affecting large T or small t antigen with respect to kinetics at 39.8 degrees C of entry into S phase and cellular proliferation. Three mutants, 3Y1tsD123, 3Y1tsF121 and 3Y1tsG125, expressed T antigen and entered S phase at 39.8 degrees C from both the arrested states after infection with either wild-type, tsA mutants, or a .54/.59 deletion mutant of SV40, whereas in the density-arrested 3Y1tsH203, expression of T antigen and entry into S phase were inefficient and ts. Following the WT-SV40 induced entry into S phase, the temperature-arrested 3Y1tsD123 detached from the substratum with no detectable increase in cell number, whereas the density-arrested ones completed a round of the cell cycle and then detached. 3Y1tsF121 and 3Y1tsG125 in the both arrested states proliferated through more than one generation. 3Y1tsF121 and 3Y1tsG125 in the density-arrested state infected with tsA mutants once proliferated and then ceased to increase in number as the percentage of T-antigen positive population decreased. These results suggest that wild-type and tsA-mutated large T antigens are able to overcome the cellular ts blocks of entry into S phase in the 3 ts mutants of 3Y1 cells in both the arrested states, and that small t antigen is not required to overcome the blocks. It is also suggested that cellular behaviors subsequent to S phase (viability, mitosis, and proliferation in the following generations) depend on cellular arrest states, on traits of cellular ts defects, and on the duration of large T antigen expression.
Induction of Gene Expression as a Monitor of Exposure to Ionizing Radiation (2001)

The complex molecular responses to genotoxic stress are mediated by a variety of regulatory pathways. The transcription factor TP53 plays a central role in the cellular response to DNA-damaging agents such as ionizing radiation, but other pathways also play important roles. In addition, differences in radiation quality, such as the exposure to high-LET radiation that occurs during space travel, may influence the pattern of responses. The premise is developed that stress gene responses can be employed as molecular markers for radiation exposure using a combination of informatics and functional genomics approaches. Published studies from our laboratory have already demonstrated such transcriptional responses with doses of gamma rays as low as 2 cGy, and in peripheral blood lymphocytes (PBLs) irradiated ex vivo with doses as low as 20 cGy. We have also found several genes elevated in vivo 24 h after whole-body irradiation of mice with 20 cGy. Such studies should provide insight into the molecular responses to physiologically relevant doses, which cannot necessarily be extrapolated from high-dose studies. In addition, ongoing experiments are identifying large numbers of potential biomarkers using microarray hybridization and various irradiation protocols including expression at different times after exposure to low- and high-LET radiation. Computation-intensive informatics analysis methods are also being developed for management of the complex gene expression profiles resulting from these experiments. With further development of these approaches, it may be feasible to monitor changes in gene expression after low-dose radiation exposure and other physiological stresses that may be encountered during manned space flight, such as the planned mission to Mars.
Stochastic Resonance Effects on Apnea, Bradycardia, and Oxygenation: A Randomized Controlled Trial (2015)

SR stimulation may be a noninvasive and nonpharmacologic treatment option for apnea, oxygen desaturation, and some aspects of bradycardia in premature infants.
MDM2 is a Central Node in the p53 Pathway: 12 Years and Counting (2005)

Twelve years ago, the Mdm2 oncogene was shown to bind to and inhibit the tumor suppressor protein, p53. During the past 12 years, both genetic and biochemical studies have demonstrated that Mdm2 is a key negative regulator of the tumor suppressor p53. Mdm2 and p53 form an oscillating auto-regulatory feedback loop, which is tightly controlled to allow the appropriate response to environmental stresses in order to suppress tumor formation. When Mdm2 activity is inappropriately heightened, as it is in many human tumors, p53 activity is attenuated and tumor susceptibility arises. The p53 gene is mutated in 50% of all human tumors, but in those tumors that retain wild type p53, inhibiting Mdm2 activity could activate p53 tumor suppression and therefore provide a therapeutic strategy for the treatment of cancer.
Survival of Infants With Persistent Pulmonary Hypertension Without Extracorporeal Membrane Oxygenation (1989)

A retrospective evaluation was performed of the survival after conservative therapy of infants with persistent pulmonary hypertension who met the published criteria of Bartlett et al (Pediatrics. 1985;76:479-487) or Short et al (Clinics in Perinatology. 1987;14:737-748) for extracorporeal membrane oxygenation (ECMO) therapy. An 80% to 90% mortality rate can be predicted with these criteria, which are based on historical data, if ECMO is not used. The records of infants with the diagnosis of persistent pulmonary hypertension, weighing greater than 2 kg at birth and who were treated during two time periods, January 1980 to December 1981 [23 patients] and January 1986 to December 1988 [17 patients], were reviewed. During the earlier period, hyperventilation was the mainstay of our therapy, whereas during the later period, a more conservative approach (avoidance of hyperventilation) was adopted. In 1980 to 1981, 1 of the 6 patients (17%) who were eligible for ECMO by criteria of Bartlett et al survived, which is consistent with the published data. However, in 1986 to 1988, 9 of 10 ECMO-eligible patients (90%) survived (P less than .02). The corresponding survival figures using the alveolar-arterial oxygen difference criteria of Short et al were 0 of 5 survivors (0%) in 1980 to 1981 and 8 of 9 (89%) in 1986 to 1988 (P less than .006). These data indicate that approximately 90% of patients who are candidates for ECMO now survive in our institution without the use of that therapy.(ABSTRACT TRUNCATED AT 250 WORDS)
Transport of β-Casein-derived Peptides by the Oligopeptide Transport System Is a Crucial Step in the Proteolytic Pathway of Lactococcus lactis (1995)

In the proteolytic pathway of Lactococcus lactis, milk proteins (caseins) are hydrolyzed extracellularly to oligopeptides by the proteinase (PrtP). The fate of these peptides, i.e. extracellular hydrolysis followed by amino acid uptake or transport followed by intracellular hydrolysis, has been addressed. Mutants have been constructed that lack a functional di-tripeptide transport system (DtpT) and/or oligopeptide transport system (Opp) but do express the P1-type proteinase (specific for hydrolysis of beta- and to a lesser extent kappa-casein). The wild type strain and the DtpT- mutant accumulate all beta-casein-derived amino acids in the presence of beta-casein as protein substrate and glucose as a source of metabolic energy. The amino acids are not accumulated significantly inside the cells by the Opp- and DtpT- Opp- mutants. When cells are incubated with a mixture of amino acids mimicking the composition of beta-casein, the amino acids are taken up to the same extent in all four strains. Analysis of the extracellular peptide fraction, formed by the action of PrtP on beta-casein, indicates that distinct peptides disappear only when the cells express an active Opp system. These and other experiments indicate that (i) oligopeptide transport is essential for the accumulation of all beta-casein-derived amino acids, (ii) the activity of the Opp system is sufficiently high to support high growth rates on beta-casein provided leucine and histidine are present as free amino acids, and (iii) extracellular peptidase activity is not present in L. lactis.
Milk Fat Globule EGF-8 Promotes Melanoma Progression through Coordinated Akt and Twist Signaling in the Tumor Microenvironment (2008)

The pathogenesis of malignant melanoma involves the interplay of tumor cells with normal host elements, but the underlying mechanisms are incompletely understood. Here, we show that milk fat globule EGF-8 (MFG-E8), a secreted protein expressed at high levels in the vertical growth phase of melanoma, promotes disease progression through coordinated alpha(v)beta(3) integrin signaling in the tumor microenvironment. In a murine model of melanoma, MFG-E8 enhanced tumorigenicity and metastatic capacity through Akt-dependent and Twist-dependent pathways. MFG-E8 augmented melanoma cell resistance to apoptosis, triggered an epithelial-to-mesenchymal transition (EMT), and stimulated invasion and immune suppression. In human melanoma cells, MFG-E8 knockdown attenuated Akt and Twist signaling and thereby compromised tumor cell survival, EMT, and invasive ability. MFG-E8-deficient human melanoma cells also showed increased sensitivity to small molecule inhibitors of insulin-like growth factor I receptor and c-Met. Together, these findings delineate pleiotropic roles for MFG-E8 in the tumor microenvironment and raise the possibility that systemic MFG-E8 blockade might prove therapeutic for melanoma patients.