Miracle-dz/UniFAR-FTUs huggingface dataset:
MHC Class I Family Proteins Retard Systemic Lupus Erythematosus Autoimmunity and B Cell Lymphomagenesis

Dysregulation of the T cell-dependent Ab response can lead to numerous immunological disorders, ranging from systemic lupus erythematosus to B cell lymphomas. Cellular processes governed by MHC class II proteins play a major role in this response and its dysregulation. The extent to which processes controlled by the diverse family of MHC class I proteins impact such autoimmune and neoplastic disorders, however, is less clear. In this study, we genetically dissect the contributions of individual MHC class I family members and the pathological processes under their control in the systemic lupus erythematosus-like disease of BXSB.Yaa mice and B cell lymphomagenesis of SJL mice. This study reveals a powerful repressive regulatory axis comprised of MHC class I-dependent CD8+ T cells and NK cells. These results indicate that the predominant role of the MHC class I protein family in such immunological disorders is to protect from more aggressive diseases.
Differential Activation of NK Cells by Influenza A Pseudotype H5N1 and 1918 and 2009 Pandemic H1N1 Viruses

ABSTRACT Natural killer (NK) cells are the effectors of innate immunity and are recruited into the lung 48 h after influenza virus infection. Functional NK cell activation can be triggered by the interaction between viral hemagglutinin (HA) and natural cytotoxicity receptors NKp46 and NKp44 on the cell surface. Recently, novel subtypes of influenza viruses, such as H5N1 and 2009 pandemic H1N1, transmitted directly to the human population, with unusual mortality and morbidity rates. Here, the human NK cell responses to these viruses were studied. Differential activation of heterogeneous NK cells (upregulation of CD69 and CD107a and gamma interferon [IFN-γ] production as well as downregulation of NKp46) was observed following interactions with H5N1, 1918 H1N1, and 2009 H1N1 pseudotyped particles (pps), respectively, and the responses of the CD56dim subset predominated. Much stronger NK activation was triggered by H5N1 and 1918 H1N1 pps than by 2009 H1N1 pps. The interaction of pps with NK cells and subsequent internalization were mediated by NKp46 partially. The NK cell activation by pps showed a dosage-dependent manner, while an increasing viral HA titer attenuated NK activation phenotypes, cytotoxicity, and IFN-γ production. The various host innate immune responses to different influenza virus subtypes or HA titers may be associated with disease severity.
Distinct RNA-dependent RNA polymerases are required for RNAi triggered by double-stranded RNA versus truncated transgenes in Paramecium tetraurelia

In many eukaryotes, RNA-dependent RNA polymerases (RdRPs) play key roles in the RNAi pathway. They have been implicated in the recognition and processing of aberrant transcripts triggering the process, and in amplification of the silencing response. We have tested the functions of RdRP genes from the ciliate Paramecium tetraurelia in experimentally induced and endogenous mechanisms of gene silencing. In this organism, RNAi can be triggered either by high-copy, truncated transgenes or by directly feeding cells with double-stranded RNA (dsRNA). Surprisingly, dsRNA-induced silencing depends on the putatively functional RDR1 and RDR2 genes, which are required for the accumulation of both primary siRNAs and a distinct class of small RNAs suggestive of secondary siRNAs. In contrast, a third gene with a highly divergent catalytic domain, RDR3, is required for siRNA accumulation when RNAi is triggered by truncated transgenes. Our data further implicate RDR3 in the accumulation of previously described endogenous siRNAs and in the regulation of the surface antigen gene family. While only one of these genes is normally expressed in any clonal cell line, the knockdown of RDR3 leads to co-expression of multiple antigens. These results provide evidence for a functional specialization of Paramecium RdRP genes in distinct RNAi pathways operating during vegetative growth.
Collective Motion, Sensor Networks, and Ocean Sampling

This paper addresses the design of mobile sensor networks for optimal data collection. The development is strongly motivated by the application to adaptive ocean sampling for an autonomous ocean observing and prediction system. A performance metric, used to derive optimal paths for the network of mobile sensors, defines the optimal data set as one which minimizes error in a model estimate of the sampled field. Feedback control laws are presented that stably coordinate sensors on structured tracks that have been optimized over a minimal set of parameters. Optimal, closed-loop solutions are computed in a number of low-dimensional cases to illustrate the methodology. Robustness of the performance to the influence of a steady flow field on relatively slow-moving mobile sensors is also explored
Stormwater Inputs in Urban Streams: Impact and Persistence of Effects on Stream Temperature

Stream temperature is an important metric for determining the health of a stream system, and derived from complex interactions between climate, weather, and local landscape characteristics. In urban areas, stream temperature is additionally influenced by impervious surfaces as well as stormwater infrastructure that translates water quickly to stream channels. Disentangling the impacts of spatial and temporal drivers of the stream temperature regime is therefore a complex task. To improve understanding of spatial and temporal variability in stream temperatures, we combined in situ stream temperature loggers with thermal infrared (TIR) imagery collected via unmanned aerial vehicles (UAV) along a 2.25 km section of creek in Syracuse, NY. TIR imagery was used document the heterogeneity of stream temperature as impacted by a natural spring and several stormwater inputs across the stream channel and down the length of a stream for three flights in May, June, and July of 2017. Thermal heterogeneities derived from stormwater culverts were observed to persist as far as 290 m downstream from their source depending on the time of year. Reach observations and weather station data were combined with TIR imagery to calibrate a deterministic stream temperature model using a modified version of HFLUX 3.0. Stream temperatures were simulated in HFLUX for a five-day period, after a two day warm up, surrounding monthly flights using different combinations of stormwater discharge and temperature. The use of two metrics derived from the TIR data, an ‘Initial Impact’ (on stream temperature) and ‘Effect Duration’, enabled spatial model calibration alongside temporal calibration to iButton observations at the end of the reach. Discrepancies between best models fits through space and best model fits through time establish that model approaches should incorporate errors in multiple dimensions. Overall, this study demonstrates that stormwater inputs in northeastern watersheds may cool mean stream temperatures, with effects that can persist for hundreds of meters downstream. Beyond the impact of stormwater, we also show that UAV-based TIR can be particularly useful for documenting these impacts when paired with in situ sensors. Finally, we find that calibrating models in multiple dimensions can more accurately simulate spatio-temporal hydrologic processes and mixing between urban water sources and the main channel. Stormwater Inputs in Urban Streams: Impact and Persistence of Effects on Stream Temperature
Magnetoencephalography in Presurgical Evaluation of Children with the Landau‐Kleffner Syndrome

Summary: Purpose: Our aim was (a) to localize the primary epileptogenic cortex for possible multiple subpial transsection in four children with the Landau‐Kleffner syndrome (LKS), and (b) to evaluate the impact of magnetoencephalography (MEG) in the localizing process.
Injuries of the cervical spine in patients with ankylosing spondylitis: experience at two trauma centers.

OBJECT The cervical spine in a patient with ankylosing spondylitis (AS) (Bechterew disease) is exposed to maximal risk due to physical load. Even minor trauma can cause fractures because of the spine's poor elasticity (so-called bamboo spine). The authors conducted a study to determine the characteristics of cervical fractures in patients with AS to describe the standard procedures in the treatment of this condition at two trauma centers and to discuss complications of and outcomes after treatment. METHODS Between 1990 and 2006, 37 patients were surgically treated at two institutions. All patients were examined preoperatively and when being discharged from the hospital for rehabilitation. Single-session (11 cases) and two-session anterior-posterior (13 cases), anterior (11 cases), posterior (two cases), and laminectomy (one case) procedures were performed. The injury pattern, segments involved, the pre- and postoperative neurological status, and complications were analyzed. Preoperative neurological deficits were present in 36 patients. All patients experienced improvement postoperatively, and there was no case of surgery-related neurological deterioration. In patients in whom treatment was delayed because of late diagnosis, preoperative neurological deficits were more severe and improvement worse than those treated earlier. The causes of three deaths were respiratory distress syndrome due to a rigid thorax and cerebral ischemia due to rupture of the vertebral arteries. There were 12 perioperative complications (32%), three infections, one deep venous thrombosis, five early implant failures, and the three aforementioned fatalities. There were no cases of epidural hematoma. In all five cases in which early implant failure required revision surgery, the initial stabilization procedure had been anterior only. A comparison of complications and the outcomes at the two centers revealed no significant differences. CONCLUSIONS The standard intervention for these injuries is open reduction, anterior decompression and fusion, and anterior-posterior stabilization; these procedures may be conducted in one or two stages. Based on the early implant failures that occurred exclusively after single-session anterior stabilizations (five of 10--a failure rate of 50%), the authors have performed only posterior and anterior procedures since 1997 at both centers. Diagnostic investigations include computed tomography scanning or magnetic resonance imaging of the whole spine, because additional injuries are common. The causative trauma may be very slight, and diagnosis may be delayed because plain radiographs can be initially misinterpreted. In cases in which diagnosis is delayed, patients present with more severe neurological deficits, and postoperative improvement is less pronounced than that in patients in whom a prompt diagnosis is established. Because of postoperative pulmonary and ischemic complications, the mortality rate is high. In the present series the mortality rate was lower than the mean rate reported in the literature.
Les zones de décrochement et les virgations structurales en Iran . Conséquences des résultats de l'analyse structurale de Qom.

Les principales directions structurales de l'Iran peuvent etre regroupees en trois grandes orientations fondamentales : NW-SE, NE-SW et N-S. Toutes les zones ainsi definies comportent des structures elementaires caracteristiques de comportements en decrochement. Ces mouvements decrochants sur les grands accidents d'un domaine composite peuvent etre relies aux deplacements des grands blocs cratoniques adjacents. Les composantes de deplacement tangentiel (~) ou de serrage (a) de chacune des zones de decrochement, sont conditionnees par la valeur de l'angle (~) entre la direction de deplacement des grands blocs et celle des failles initiales limitant les bassins de sedimentation (dont les dispositions sont elles-meme sous la dependance de ce regime de deplacements dans un domaine fracture). Il s'ensuit que selon leur orientation vis a vis des deplacements, dans un regime pourtant equivalent, les differentes zones structurales iraniennes sont plus ou moins sujettes a l'aplatissement. L'une des plus longues zones structurales de l'Iran et des plus fracturees est la cicatrice eruptive de Tabriz-Bazman. C'est celle qui a ete choisie pour servir d'exemple dans l'etude du role des decrochements en Iran. L'analyse a l'echelle regionale des structures de cette cicatrice, a ete faite a l'aide des documents actuellement disponibles dans la litterature et de quelques travaux personnels ponctuels. Parmi ceux-ci on insiste sur l'exemple particulierement instructif de la virgation de Qom qui a ete analysee en detail. En effet les fractures majeures de la zone de Tabriz-Bazman correspondent a un reseau d'un systeme en decrochement allant jusqu'aux accidents de troisieme ordre. Quoique la zone soit actuellement decalee par ces failles d'ordre inferieur selon une direction moyenne N 145, elle s'organise en fait en un grand couloir de decrochement dextre d'orientation N 125-130. Les virgations d'axes de plis, les lentilles de cisaillement elementaires, les failles courbes . sont les structures les plus demonstratives de ce systeme. La virgation de la region de Qom est exemplaire a cet egard. Toutes ces structures indiquent un cisaillement dextre accompagne d'un aplatissement. Le modele cinematique interpretatif ainsi defini, a ete verifie par des essais sur modele analogique. Le dispositif experimental est decrit, qui permet d'envisager les differents cas ou la valeur de l'angle (-) , entre direction de deplacement et limites des bassins intervient. On tente en conclusion de generaliser ce modele a l'ensemble de l'Iran et on montre que l'etat de deformation de chaque zone structurale est sous la dependance desgrandes directions fondamentales et de l'orientation des deplacements des plaques adjacentes.
N-way model merging

Model merging is widely recognized as an essential step in a variety of software development activities. During the process of combining a set of related products into a product line or consolidating model views of multiple stakeholders, we need to merge multiple input models into one; yet, most of the existing approaches are applicable to merging only two models. In this paper, we define the n-way merge problem. We show that it can be reduced to the known and widely studied NP-hard problem of weighted set packing. Yet, the approximation solutions for that problem do not scale for real-sized software models. We thus evaluate alternative approaches of merging models that incrementally process input models in small subsets and propose our own algorithm that considerably improves precision over such approaches without sacrificing performance.
The percentage of serum thyroglobulin rise in the first-week did not predict the eventual success of high-intensity focussed ablation (HIFU) for benign thyroid nodules

Abstract Background: Given that high-intensity focussed ultrasound (HIFU) of benign thyroid nodules often causes a massive release of thyroglobulin (Tg) into the circulation, we hypothesised a greater initial Tg rise may result in a greater nodule shrinkage 6 months after ablation. Methods: One hundred and five patients who underwent HIFU for symptomatic benign thyroid nodule from 2015 to 2016 were analysed. Serum Tg and anti-Tg autoantibody were checked on treatment day (baseline) and 4 d after treatment. The % of Tg rise = [serum Tg on day-4 – baseline serum Tg]/[baseline serum Tg] * 100 while the nodule shrinkage as measured by volume reduction ratio (VRR) = [baseline volume – volume at 6-month]/[baseline volume] * 100. Treatment success was defined as VRR >50%. Results: At 6-month, the mean VRR was 62.2 ± 25.0% and 59 (76.6%) patients had treatment success. The mean baseline Tg level increased from 292.8 ± 672.7 ng/mL to 2022.7 ± 1759.8 ng/mL in the first-week. The % of Tg rise did not significantly correlate with either 3-month or 6-month VRR (p = 0.920 and p = 0.699, respectively). The mean % of Tg rise in the first week was not different between those with and without 6-month treatment success (368.2% vs. 1068.7%, p = 0.381). No clinical factors significantly correlated with treatment success. Conclusions: There was an almost seven-fold increase in the mean Tg level 4 d after HIFU ablation. The % of Tg rise in the first week did not appear to correlate with the 6-month nodule shrinkage or treatment success.
Spermatozoa and seminal plasma fatty acids as predictors of cryopreservation success

There is a lack of information about the importance of fatty acid composition of the human sperm membranes and seminal plasma in the cryopreservation procedure. Our aims were to study the possible relationships between the fatty acid composition of human spermatozoa or seminal fluid before freezing, and the sperm quality, measured in terms of viability and motility, before and after freezing–thawing. A further objective of this study was to determine whether the antioxidant capacity (TAC) of the seminal plasma is related to fatty acid (FA) composition and to success of the cryopreservation process. Polyunsaturated fatty acids (PUFA), ω3 PUFAs and docosahexaenoic acid (DHA) in spermatozoa were significantly positively correlated with sperm viability and motility parameters before and after freezing. An inverse relationship was found for monounsaturated (MUFA), ratio ω6/ω3, ratio saturated saturated fatty acids/PUFA (SFA/PUFA) with the seminal parameters. Seminal plasma fatty acid composition was not related to viability. However, motility parameters before and after freezing were related to stearic acid (C18:0) and DHA. TAC in seminal plasma was directly related to PUFA, w3 and DHA. On the other hand, SFA, C22:0, C24:0 and MUFA in seminal plasma were inversely related to the antioxidant capacity. TAC was directly correlated with motion parameters after thawing, We described a significant correlation between the fatty acid composition of the human spermatozoa or seminal plasma and the sperm parameters of the samples after thawing. PUFA, W3 and specially DHA are directly correlated with sperm motility and viability after freezing/thawing, and MUFA was inversely correlated. This means that in the future the fatty acid composition could be used as a predictor of the capacity of cryopreservation. On the other hand, we could design further procedures to modify the lipid composition or/and antioxidant capacity of ejaculate to make it more resistant to the cryopreservation process.
The five-repetition sit-to-stand test as a functional outcome measure in COPD

Background Moving from sitting to standing is a common activity of daily living. The five-repetition sit-to-stand test (5STS) is a test of lower limb function that measures the fastest time taken to stand five times from a chair with arms folded. The 5STS has been validated in healthy community-dwelling adults, but data in chronic obstructive pulmonary disease (COPD) populations are lacking. Aims To determine the reliability, validity and responsiveness of the 5STS in patients with COPD. Methods Test-retest and interobserver reliability of the 5STS was measured in 50 patients with COPD. To address construct validity we collected data on the 5STS, exercise capacity (incremental shuttle walk (ISW)), lower limb strength (quadriceps maximum voluntary contraction (QMVC)), health status (St George's Respiratory Questionnaire (SGRQ)) and composite mortality indices (Age Dyspnoea Obstruction index (ADO), BODE index (iBODE)). Responsiveness was determined by measuring 5STS before and after outpatient pulmonary rehabilitation (PR) in 239 patients. Minimum clinically important difference (MCID) was estimated using anchor-based methods. Results Test-retest and interobserver intraclass correlation coefficients were 0.97 and 0.99, respectively. 5STS time correlated significantly with ISW, QMVC, SGRQ, ADO and iBODE (r=−0.59, −0.38, 0.35, 0.42 and 0.46, respectively; all p<0.001). Median (25th, 75th centiles) 5STS time decreased with PR (Pre: 14.1 (11.5, 21.3) vs Post: 12.4 (10.2, 16.3) s; p<0.001). Using different anchors, a conservative estimate for the MCID was 1.7 s. Conclusions The 5STS is reliable, valid and responsive in patients with COPD with an estimated MCID of 1.7 s. It is a practical functional outcome measure suitable for use in most healthcare settings.
Who needs an artificial pancreas? (怎样的患者需要一个人工胰腺？)

The development of a closed‐loop “artificial pancreas” would be a welcome advance for both endocrinologists and diabetic patients struggling to attain near normal glycemic control. While great strides in automatically controlling blood sugar in the fasting, sedentary state have been made through complex mathematical modeling, management of blood sugar excursions due to food and exercise have been more problematic. An artificial pancreas is not feasible at this time because of limitations inherent in the currently available technology.
Locating All the Global Minima Using Multi-Species Particle Swarm Optimizer: The Inertia Weight and The Constriction Factor Variants

This paper reports further simplification and improvement of a modified particle swarm optimizer (PSO) called the multi-species particle swarm optimizer (MSPSO) proposed by the author. MSPSO extends the original PSO by dividing the particle swarm spatially into a multiple cluster called a species in a multi-dimensional search space. Each species explores a different area of the search space and tries to find out the global or local optima of that area. Therefore it can be used to locate all the global minima of multi-modal functions in parallel. The previous version of MSPSO relies strongly on the inertia-weight annealing and its performance depends on the annealing schedule. In this paper, instead, we use the constriction factor proposed by Clerc. Our new MSPSO could locate, for example, all 18 global optima of the two-dimensional Shubert function, yet it is free from annealing-schedule optimization of the inertia weight.
Evidence on the Management of Earnings Components

Although recent studies provide convincing evidence that firms manage earnings to achieve certain reporting objectives, there is only limited evidence on what steps firms take to manage their earnings. This paper presents evidence as to which components firms use to manage bottom-line, reported earnings. Specifically, we identify a set of firms believed to be managing earnings upward; plot the empirical distributions of analysts' forecast errors for sales, operating expenses, nonoperating expenses, and depreciation expense; and then examine these distributions for discontinuities around zero. Results suggest that these firms managed earnings upward by managing sales upward and by managing operating expenses downward. There is no evidence to suggest that these firms managed nonoperating expenses or depreciation expense to affect earnings. We then identify firm characteristics (level of current assets, level of current liabilities, and operating margin percentage) that affect the likelihood that these firms used a specific component to manage earnings. Finally, we use a firm's stock recommendation to make predictions about its incentives to manage earnings. Our evidence suggests that firms rated buy (rated sell) manage earnings upward (downward) by managing sales, operating, and nonoperating expenses in predictable directions.