Miracle-dz/UniFAR-FTUs huggingface dataset:
Properties of antigen-specific suppressive T-cell factor in the regulation of antibody response of the mouse. I. In vivo activity and immunochemical characterization

An antigen-specific suppressive T-cell factor was extracted from physically disrupted thymocytes and spleen cells of mice that had been immunized with soluble protein antigens. The factor, when inoculated into syngeneic normal mice, could induce a significant suppression of IgG antibody response against a hapten coupled to the carrier protein by which the donor of the suppressor factor was immunized. The suppressor factor was found only effective in suppressing the antibody response of syngeneic or H-2 histocompatible recipients. The suppressive T-cell factor was removed by absorption with immunoadsorbent composed of the relevant antigen, but not with any of those of anti-immunoglobulin antibodies. The factor was successfully removed by alloantibodies with specificity for the K end (H-2K, I-A and I-B) of the H-2 complex of the donor strain, but not by those for the D end (I-C, SsSlp, and H-2D). The activity was removed by absorption with a heterologous antithymocyte serum. The mol wt of the suppression T- cell factor was between 35,000 and 60,000 as determined by Sephadex G- 200 gel filtration. The suppressive T-cell factor was found to be a heat-liable protein.
Dynamic programming algorithm for rate-distortion optimized media streaming

We propose a dynamic programming algorithm for finding optimal transmission policies for a single packet in rate-distortion optimized media streaming. The algorithm relies on an optimality assumption holding in particular when both the forward and round trip times have exponential distributions. In the other cases, we use the assumption as a heuristic principle. Simulations show that for realistic channel models, the algorithm provides optimal solutions and can be significantly faster than the previous fastest exact algorithm. The proposed algorithm can be used as a preprocessing step for streaming mutually dependent packets.
Aggregate-Max Nearest Neighbor Searching in the Plane

We study the aggregate/group nearest neighbor searching for the MAX operator in the plane. For a set $P$ of $n$ points and a query set $Q$ of $m$ points, the query asks for a point of $P$ whose maximum distance to the points in $Q$ is minimized. We present data structures for answering such queries for both $L_1$ and $L_2$ distance measures. Previously, only heuristic and approximation algorithms were given for both versions. For the $L_1$ version, we build a data structure of O(n) size in $O(n\log n)$ time, such that each query can be answered in $O(m+\log n)$ time. For the $L_2$ version, we build a data structure in $O(n\log n)$ time and $O(n\log \log n)$ space, such that each query can be answered in $O(m\sqrt{n}\log^{O(1)} n)$ time, and alternatively, we build a data structure in $O(n^{2+\epsilon})$ time and space for any $\epsilon>0$, such that each query can be answered in $O(m\log n)$ time. Further, we extend our result for the $L_1$ version to the top-$k$ queries where each query asks for the $k$ points of $P$ whose maximum distances to $Q$ are the smallest for any $k$ with $1\leq k\leq n$: We build a data structure of O(n) size in $O(n\log n)$ time, such that each top-$k$ query can be answered in $O(m+k\log n)$ time.
Spatial and Temporal Dynamics of Larval Fish Assemblages in the Strait of Georgia

Supervisory Committee Dr. John F. Dower, Supervisor (Department of Biology) Dr. Verena Tunnicliffe, Departmental Member (Department of Biology) Dr. Pierre Pepin, Departmental Member (Department of Biology) Dr. David L. Mackas, Outside Member (Institute of Ocean Sciences, Fisheries and Oceans Canada) Dr. Steward M. McKinnell, Additional Member (North Pacific Marine Science Organization) For marine fishes, the early larval phase is considered a critical stage for survivorship and recruitment. The spatial and temporal dynamics of larval fish assemblages can influence their success and trophic structure of marine communities and entire ecosystems. This thesis will provide the first characterization of larval fish assemblage in the Strait of Georgia (SoG) in terms of diversity, abundance and composition, and their variability over multiple temporal scales, as well as the first quantification of variability in larval fish distribution in the SoG across multiple spatial scales. On the interdecadal scale, a significant decrease in larval abundance of several dominant fish taxa (Pacific hake, walleye Pollock, northern smoothtongue and rockfishes) contributed to a decline in total larval abundance and turnover in the composition structure between the early 1980s and the late 2000s. In contrast, both abundance and the relative composition of flatfishes and several demersal forage fish taxa increased during the same period. On interannual scales, abundance, diversity and community structure of the spring larval assemblages varied dramatically through 2007-2010, a period which alternated between strong La Niña and El Niño events. Higher overall larval concentrations were associated with warm conditions in the SoG in 2007 and 2010, while the lowest larval concentration was associated with cooler condition in 2009. Examination of associations between larval fish assemblages and environmental fluctuations suggests a potential influence of large-scale climate processes between the early 1980s and the late 2000s, but a primary association with local environmental
Preliminary analysis of physiological changes of nursing students during training

Long-term exposure to stress has been associated with chronic diseases, depression, and immune disorders. The precise detection and assessment of stress depends on personalized physiological monitoring and assessment of influence of personal and workplace factors We monitored nursing students during training on a high fidelity simulator in the Real-time Physiological Monitoring Lab at the University of Alabama in Huntsville. In this paper we present the preliminary results of this pilot study. A total of 14 participants were recorded: 12 female and 2 male subjects, 23-46 years old with an average age of 32.8 years. We analyzed heart rate, Heart Rate Variability (HRV), respiration, and physical activity. The results indicate significant strain on subjects during simulation: heart rate increased 16.7%, from 82.8 to 96.6 bpm (p<;0.001), falling to a slightly increased level after the training session (84.9 bpm); Root Mean Square of Successive RR Differences (RMSSD) decreased from 38.9 ms to 37.7 ms; the breathing rate increased during the simulation from 16.9 to 17.7 breaths/min. Distractions also significantly influenced physiological parameters: the first telephone call increased heart rate on average 9 bpm (p<;0.001), while the second call increased heart rate 8.6 bpm (p<;0.001). The simulated patient-related events created even more prominent response; the average heart rate increased 17.4 bpm (p<;0.001) at the onset of “patient in crisis” event. Real-time wearable monitoring may provide assessment of occupational stress.
R Factor-Mediated and Chromosomal Resistance to Ampicillin in Escherichia coli

Sixty-four ampicillin-resistant strains of Escherichia coli were studied. Six characters were examined: (i) resistance to ampicillin, cephalothin, and carbenicillin, (ii) synergy between ampicillin and cloxacillin, (iii) level of β-lactamase activity after osmotic shock, (iv) transferability of ampicillin resistance, (v) immunological characterization of the enzyme, and (vi) determination of substrate profiles. One class of strains was found in which synthesis of β-lactamase is inferred to be plasmid mediated; these strains are highly resistant to ampicillin and carbenicillin, sensitive to cephalothin, do not show synergism between ampicillin and cloxacillin, and reveal a high enzymatic activity after osmotic shock. A second class is formed by strains for which β-lactamase synthesis is inferred to be chromosomal; these strains present a low resistance level to ampicillin, are sensitive to carbenicillin and resistant to cephalothin, show a synergism between ampicillin and cloxacillin, and reveal a very low enzymatic activity after osmotic shock. These characters may be used to differentiate periplasmic and cell-bound β-lactamases.
Tree growth is better explained by absorptive fine roots than transport fine roots

Quantifying plant trait variation yields insights into trade-offs inherent in the ecological strategies of plants and is the basis for a trait-based prediction of plant performance and ecosystem functioning. Although the interest in root traits has increased in recent years, we still have limited knowledge of i) whether functionally discrete fine roots—absorptive versus transport roots—have similar trait coordination and ii) how they help to explain plant performance, such as growth. We measured traits of 28 European broadleaved tree species growing in a research arboretum to study i) the coordination within absorptive and transport fine root traits and ii) the degree of trait-tree growth relationships. To do so, we combined a suite of morphological (root diameter, specific root length and root tissue density) and anatomical (cortex to stele ratio and mycorrhizal colonization rate) traits for each of the absorptive and transport roots. Despite remarkable differences in average trait values between absorptive and transport roots, our study shows that trait coordination within absorptive and transport roots is comparable. Our results also show that tree growth is better explained by absorptive root traits than by transport roots and is higher in species with a thinner root diameter. Synthesis. The significant relationship between absorptive roots and tree growth and the lack of such a relationship for transport highlight that roots mostly involved with resource absorption are more important in explaining tree growth than roots involved in transport.
Absence of Mycoplasmal Gene in Malignant Mammalian Cells Transformed by Chronic Persistent Infection of Mycoplasmas

Abstract Chronic persistent infections by mycoplasmas induced malignant transformation of C3H mouse embryo cells that normally had never been reported to undergo spontaneous transformation. This mycoplasma-mediated oncogenic process had a long latency (more than 7 weeks of continuous mycoplasmal infection) and showed a multistage progression characterized by reversibility (at least up to 11 weeks of mycoplasmal infection) and irreversibility of malignant properties upon removal of the mycoplasma from culture. Further prolonged infections (18 weeks) by Mycoplasma fermentans or M. penetrans resulted in permanent transformation of these C3H cells that no longer required the continued presence of the transformation-inducing mycoplasmas in cultures to retain their malignant properties. Previous studies of viral oncogenesis revealed that virus-transformed cells always had viral gene(s) present. Integration of viral gene(s) apparently played an important role in the process of oncogenesis. In this study, we examined if the continued presence of any mycoplasmal gene(s) in mammalian cells, in whatever form, was also crucial in causing malignant cell transformation. Representational difference analysis (RDA) was a recently developed powerful technique to compare differences between two complex genomes. In the RDA system, subtractive and kinetic enrichment was used to purify and isolate restriction endonuclease gene f ragment(s) of mycoplasmal origin, presumably present only in mycoplasma-transformed C3H cells, but not in nonmycoplasma-exposed control C3H cells. After three rounds of subtractive hybridization following PCR enrichment for each of three different restriction enzymes DNA digests, no gene fragment of mycoplasmal origin was amplified or identified in the permanently transformed C3H cells. Differing from tumorigenesis in animal cells induced by most oncogenic viruses or in plant cells induced by Agrobacteria, mycoplasmas evidently did not cause malignant transformation by integrating their gene(s) into the mammalian cell genome.
Contextualized Topic Coherence Metrics

This article proposes a new family of LLM-based topic coherence metrics called Contextualized Topic Coherence (CTC) and inspired by standard human topic evaluation methods. CTC metrics simulate human-centered coherence evaluation while maintaining the efficiency of other automated methods. We compare the performance of our CTC metrics and five other baseline metrics on seven topic models and show that CTC metrics better reflect human judgment, particularly for topics extracted from short text collections by avoiding highly scored topics that are meaningless to humans.
A statistical model selection strategy applied to neural networks

In statistical modelling, an investigator must often choose a suitable model among a collection of viable candidates. There is no consensus in the research community on how such a comparative study is performed in a methodologically sound way. The ranking of several methods is usually performed by the use of a selection criterion, which assigns a score to every model based on some underlying statistical principles. The fitted model that is favoured is the one corresponding to the minimum (or the maximum) score. Statistical significance testing can extend this method. However, when enough pairwise tests are performed the multiplicity effect appears which can be taken into account by considering multiple comparison procedures. The existing comparison procedures can roughly be categorized as analytical or resampling based. This paper describes a resampling based multiple comparison technique. This method is illustrated on the estimate of the number of hidden units for feed-forward neural networks.
The effects of aging on the functional and structural properties of the rat basilar artery

Aging leads to progressive pathophysiological changes in blood vessels of the brain and periphery. The aim of this study was to evaluate the effects of aging on cerebral vascular function and structure. Basilar arteries were isolated from male Fischer 344 cross Brown Norway (F344xBN) rats at 3, 8, and 24 months of age. The basilar arteries were cannulated in the pressurized system (90 cm H2O). Contractile responses to KCl (30–120 mmol/L) and endothelin‐1 (10−11–10−7 mol/L) were evaluated. Responses to acetylcholine (ACh) (10−10–10−4 mol/L), diethylamine (DEA)‐NONO‐ate (10−10–10−4 mol/L), and papaverin (10−10–10−4 mol/L) were assessed to determine both endothelium‐dependent and endothelium‐independent responsiveness. Advanced aging (24 months) decreased responses of the basilar artery to both the contractile and relaxing agents; whereas, DEA‐induced dilation was significantly higher in the 8‐month‐old group compared with the younger and older groups. The arterial wall‐to‐lumen ratio was significantly increased in 24‐month‐old rats. Smooth muscle cell count was also decreased in old rats. These findings indicate that aging produces dysfunction of both the endothelium and the vascular smooth muscle in the basilar artery. Aging also alters wall structure of the basilar artery, possibly through decreases in smooth muscle cell number and concomitant hypertrophy.
Urinary tract infection

© 2010 The University of Texas Southwestern Medical Center at Dallas History Onset of symptoms Nature of symptoms (pain intensity, timing, and localization) Abnormality in urine pattern, color – frequency, nocturia, incontinence, observed hematuria Associated symptoms pelvic pain fever; chills, back pain, vaginal discharge Last menstrual period in females Sexual activity, type of contraception, symptoms in partner (if any) History of prior urinary or gynecologic symptoms and infections Other co morbid conditions Allergies Use of medications and other topical hygiene products
Overexpression of human mitochondrial valyl tRNA synthetase can partially restore levels of cognate mt-tRNAVal carrying the pathogenic C25U mutation

Phenotypic diversity associated with pathogenic mutations of the human mitochondrial genome (mtDNA) has often been explained by unequal segregation of the mutated and wild-type genomes (heteroplasmy). However, this simple hypothesis cannot explain the tissue specificity of disorders caused by homoplasmic mtDNA mutations. We have previously associated a homoplasmic point mutation (1624C>T) in MTTV with a profound metabolic disorder that resulted in the neonatal deaths of numerous siblings. Affected tissues harboured a marked biochemical defect in components of the mitochondrial respiratory chain, presumably due to the extremely low (<1%) steady-state levels of mt-tRNAVal. In primary myoblasts and transmitochondrial cybrids established from the proband (index case) and offspring, the marked respiratory deficiency was lost and steady-state levels of the mutated mt-tRNAVal were greater than in the biopsy material, but were still an order of magnitude lower than in control myoblasts. We present evidence that the generalized decrease in steady-state mt-tRNAVal observed in the homoplasmic 1624C>T-cell lines is caused by a rapid degradation of the deacylated form of the abnormal mt-tRNAVal. By both establishing the identity of the human mitochondrial valyl-tRNA synthetase then inducing its overexpression in transmitochondrial cell lines, we have been able to partially restore steady-state levels of the mutated mt-tRNAVal, consistent with an increased stability of the charged mt-tRNA. These data indicate that variations in the levels of VARS2L between tissue types and patients could underlie the difference in clinical presentation between individuals homoplasmic for the 1624C>T mutation.
Crucial Role of ROCK2 in Vascular Smooth Muscle Cells for Hypoxia-Induced Pulmonary Hypertension in Mice

Objective—Rho/Rho-kinase (ROCK) pathway in vascular smooth muscle cells (VSMCs) plays an important role in the pathogenesis of cardiovascular diseases, including pulmonary arterial hypertension (PAH). Rho-kinase has 2 isoforms, ROCK1 and ROCK2, with different functions in different cells; ROCK1 for circulating inflammatory cells and ROCK2 for the vasculature. In the present study, we aimed to examine whether ROCK2 in VSMC is involved in the pathogenesis of PAH. Approach and Results—In patients with PAH, the expression of ROCK2 was increased in pulmonary arterial media and primary pulmonary arterial smooth muscle cells when compared with controls. To investigate the role of ROCK2 in VSMC, we generated VSMC-specific heterozygous ROCK2-deficient (ROCK2+/−) mice and VSMC-specific ROCK2-overexpressing transgenic (ROCK2-Tg) mice. The extent of hypoxia-induced pulmonary hypertension was reduced in ROCK2+/− mice and was enhanced in ROCK2-Tg mice compared with respective littermates. The protein expression of ROCK activity and phosphorylated extracellular signal–regulated kinase and the number of Ki67-positive proliferating cells in the lung were reduced in ROCK2+/− mice and were increased in ROCK2-Tg mice compared with respective littermates. In cultured mouse aortic VSMC, migration and proliferation activities were reduced in ROCK2+/− mice, and migration activity was increased in ROCK2-Tg mice compared with respective littermates. In addition, in primary pulmonary arterial smooth muscle cells from a patient with PAH, ROCK2 was required for migration and proliferation through ROCK and extracellular signal–regulated kinase activation. Conclusions—ROCK2 in VSMC contributes to the pathogenesis of PAH.
Needle Steering in 3-D Via Rapid Replanning

Steerable needles have the potential to improve the effectiveness of needle-based clinical procedures such as biopsy and drug delivery by improving targeting accuracy and reaching previously inaccessible targets that are behind sensitive or impenetrable anatomical regions. We present a new needle steering system capable of automatically reaching targets in 3-D environments while avoiding obstacles and compensating for real-world uncertainties. Given a specification of anatomical obstacles and a clinical target (e.g., from preoperative medical images), our system plans and controls needle motion in a closed-loop fashion under sensory feedback to optimize a clinical metric. We unify planning and control using a new fast algorithm that continuously replans the needle motion. Our rapid replanning approach is enabled by an efficient sampling-based rapidly exploring random tree (RRT) planner that achieves orders-of-magnitude reduction in computation time compared with prior 3-D approaches by incorporating variable curvature kinematics and a novel distance metric for planning. Our system uses an electromagnetic tracking system to sense the state of the needle tip during the procedure. We experimentally evaluate our needle steering system using tissue phantoms and animal tissue ex vivo. We demonstrate that our rapid replanning strategy successfully guides the needle around obstacles to desired 3-D targets with an average error of less than 3 mm.
Maternal antenatal anxiety, postnatal stroking and emotional problems in children: outcomes predicted from pre- and postnatal programming hypotheses

Background Mothers' self-reported stroking of their infants over the first weeks of life modifies the association between prenatal depression and physiological and emotional reactivity at 7 months, consistent with animal studies of the effects of tactile stimulation. We now investigate whether the effects of maternal stroking persist to 2.5 years. Given animal and human evidence for sex differences in the effects of prenatal stress we compare associations in boys and girls. Method From a general population sample of 1233 first-time mothers recruited at 20 weeks gestation we drew a random sample of 316 for assessment at 32 weeks, stratified by reported inter-partner psychological abuse, a risk indicator for child development. Of these mothers, 243 reported at 5 and 9 weeks how often they stroked their infants, and completed the Child Behavior Checklist (CBCL) at 2.5 years post-delivery. Results There was a significant interaction between prenatal anxiety and maternal stroking in the prediction of CBCL internalizing (p = 0.001) and anxious/depressed scores (p < 0.001). The effects were stronger in females than males, and the three-way interaction prenatal anxiety × maternal stroking × sex of infant was significant for internalizing symptoms (p = 0.003). The interactions arose from an association between prenatal anxiety and internalizing symptoms only in the presence of low maternal stroking. Conclusions The findings are consistent with stable epigenetic effects, many sex specific, reported in animal studies. While epigenetic mechanisms may be underlying the associations, it remains to be established whether stroking affects gene expression in humans.