Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling the Zeeman effect in high-altitude SSMIS channels for numerical weather prediction profiles: comparing a fast model and a line-by-line model

Abstract. We present a comparison of a reference and a fast radiative transfer model using numerical weather prediction profiles for the Zeeman-affected high-altitude Special Sensor Microwave Imager/Sounder channels 19–22. We find that the models agree well for channels 21 and 22 compared to the channels' system noise temperatures (1.9 and 1.3 K, respectively) and the expected profile errors at the affected altitudes (estimated to be around 5 K). For channel 22 there is a 0.5 K average difference between the models, with a standard deviation of 0.24 K for the full set of atmospheric profiles. Concerning the same channel, there is 1.2 K on average between the fast model and the sensor measurement, with 1.4 K standard deviation. For channel 21 there is a 0.9 K average difference between the models, with a standard deviation of 0.56 K. Regarding the same channel, there is 1.3 K on average between the fast model and the sensor measurement, with 2.4 K standard deviation. We consider the relatively small model differences as a validation of the fast Zeeman effect scheme for these channels. Both channels 19 and 20 have smaller average differences between the models (at below 0.2 K) and smaller standard deviations (at below 0.4 K) when both models use a two-dimensional magnetic field profile. However, when the reference model is switched to using a full three-dimensional magnetic field profile, the standard deviation to the fast model is increased to almost 2 K due to viewing geometry dependencies, causing up to ±7 K differences near the equator. The average differences between the two models remain small despite changing magnetic field configurations. We are unable to compare channels 19 and 20 to sensor measurements due to limited altitude range of the numerical weather prediction profiles. We recommended that numerical weather prediction software using the fast model takes the available fast Zeeman scheme into account for data assimilation of the affected sensor channels to better constrain the upper atmospheric temperatures.
Selectivity of Pesticides used in Integrated Apple Production to the Lacewing, Chrysoperla externa

Abstract This research aimed to assess the toxicity of the pesticides abamectin 18 CE (0.02 g a.i. L-1), carbaryl 480 SC (1.73 g a.i. L-1), sulfur 800 GrDA (4.8 g a.i. L-1), fenitrothion 500 CE (0.75 g a.i. L-1), methidathion 400 CE (0.4 g a.i. L-1), and trichlorfon 500 SC (1.5 g a.i. L-1) as applied in integrated apple production in Brazil on the survival, oviposition capacity, and egg viability of the lacewing, Chrysoperla externa (Hagen) (Neuroptera: Chrysopidae) from Bento Gonçalves and Vacaria, Rio Grande do Sul State, Brazil. An attempt was made to study morphological changes caused by some of these chemicals, by means of ultrastructural analysis, using a scanning electronic microscope. Carbaryl, fenitrothion, and methidathion caused 100% adult mortality for both populations, avoiding evaluation of pesticides' effects on predator reproductive parameters. Abamectin and sulfur also affected the survival of these individuals with mortality rates of 10% and 6.7%, respectively, for adults from Bento Gonçalves, and were harmless to those from Vacaria at the end of evaluation. Trichlorfon was also harmless to adults from both populations. No compound reduced oviposition capacity. C. externa from Vacaria presented higher reproductive potential than those from Bento Gonçalves. In relation to egg viability, sulfur was the most damaging compound to both populations of C. externa. Ultrastructural analyses showed morphological changes in the micropyle and the chorion of eggs laid by C. externa treated with either abamectin or sulfur. The treatment may have influenced the fertilization of C. externa eggs and embryonic development. Sulfur was responsible for malformations in the end region of the abdomen and genitals of treated females. When applied to adults, abamectin, sulfur, and trichlorfon were harmless, while carbaryl, fenitrothion, and methidathion were harmful, according to the IOBC classification.
Stream-based Translation Models for Statistical Machine Translation

Typical statistical machine translation systems are trained with static parallel corpora. Here we account for scenarios with a continuous incoming stream of parallel training data. Such scenarios include daily governmental proceedings, sustained output from translation agencies, or crowd-sourced translations. We show incorporating recent sentence pairs from the stream improves performance compared with a static baseline. Since frequent batch retraining is computationally demanding we introduce a fast incremental alternative using an online version of the EM algorithm. To bound our memory requirements we use a novel data-structure and associated training regime. When compared to frequent batch retraining, our online time and space-bounded model achieves the same performance with significantly less computational overhead.
Maturation Pathways of Cross-Reactive HIV-1 Neutralizing Antibodies

Several human monoclonal antibodies (hmAbs) and antibody fragments, including the best characterized in terms of structure-function b12 and Fab X5, exhibit relatively potent and broad HIV-1 neutralizing activity. However, the elicitation of b12 or b12-like antibodies in vivo by vaccine immunogens based on the HIV-1 envelope glycoprotein (Env) has not been successful. B12 is highly divergent from the closest corresponding germline antibody while X5 is less divergent. We have hypothesized that the relatively high degree of specific somatic hypermutations may preclude binding of the HIV-1 envelope glycoprotein (Env) to closest germline antibodies, and that identifying antibodies that are intermediates in the pathways to maturation could help design novel vaccine immunogens to guide the immune system for their enhanced elicitation. In support of this hypothesis we have previously found that a germline-like b12 (monovalent and bivalent scFv as an Fc fusion protein or IgG) lacks measurable binding to an Env as measured by ELISA with a sensitivity in the μM range [1]; here we present evidence confirming and expanding these findings for a panel of Envs. In contrast, a germline-like scFv X5 bound Env with high (nM) affinity. To begin to explore the maturation pathways of these antibodies we identified several possible b12 intermediate antibodies and tested their neutralizing activity. These intermediate antibodies neutralized only some HIV-1 isolates and with relatively weak potency. In contrast, germline-like scFv X5 neutralized a subset of the tested HIV-1 isolates with comparable efficiencies to that of the mature X5. These results could help explain the relatively high immunogenicity of the coreceptor binding site on gp120 and the abundance of CD4-induced (CD4i) antibodies in HIV-1-infected patients (X5 is a CD4i antibody) as well as the maturation pathway of X5. They also can help identify antigens that can bind specifically to b12 germline and intermediate antibodies that together with Envs could be used as a conceptually novel type of candidate vaccines. Such candidate vaccines based on two or more immunogens could help guiding the immune system through complex maturation pathways for elicitation of antibodies that are similar or identical to antibodies with known properties.
Egocentric Social Network Structure, Health, and Pro-Social Behaviors in a National Panel Study of Americans

Using a population-based, panel survey, we study how egocentric social networks change over time, and the relationship between egocentric network properties and health and pro-social behaviors. We find that the number of prosocial activities is strongly positively associated with having more friends, or an increase in degree, with approximately 0.04 more prosocial behaviors expected for every friend added. Moreover, having more friends is associated with an improvement in health, while being healthy and prosocial is associated with closer relationships. Specifically, a unit increase in health is associated with an expected 0.45 percentage-point increase in average closeness, while adding a prosocial activity is associated with a 0.46 percentage-point increase in the closeness of one’s relationships. Furthermore, a tradeoff between degree and closeness of social contacts was observed. As the number of close social contacts increases by one, the estimated average closeness of each individual contact decreases by approximately three percentage-points. The increased awareness of the importance of spillover effects in health and health care makes the ascertainment of egocentric social networks a valuable complement to investigations of the relationship between socioeconomic factors and health.
Illegal state space identification for sequential circuit test generation

Here our new techniques are proposed to expand the known Global Illegal State (GIS) space, in order to reduce the search space. These techniques use the known GISes to generate candidate GISes, which have to be proven unjustifiable. This is an effective method to improve STPG performance because the number of stored GISes is reduced, saving memory and CPU time, while covering a larger part of the GIS space. To accelerate GIS space identification, we propose the legal state cache, to avoid useless justification repetitions. A data-structure is proposed to reduce the memory usage of the (G)ISes up to 10 times, and to accelerate GIS usage. Experimental results show a significant improvement in fault efficiency and CPU usage.
Insights from LGI1 and CASPR2 potassium channel complex autoantibody subtyping.

OBJECTIVE To determine, in patients identified as seropositive for neuronal voltage-gated potassium channel (VGKC) complex autoantibodies, the spectrum of clinical presentations and frequency of leucine-rich glioma-inactivated protein 1 (LGI1) and contactin-associated protein-like 2 (CASPR2) as defined antigenic neuronal targets in the VGKC macromolecular complex. DESIGN Retrospective cohort study. SETTING Clinical practice, Mayo Clinic Neuroimmunology Laboratory and Department of Neurology. PATIENTS A total of 54 853 patients were evaluated, of whom 1992 were found to be VGKC complex IgG positive. RESULTS From June 1, 2008, to June 30, 2010, comprehensive service serologic evaluation performed on 54853 patients with unexplained neurologic symptoms identified 1992 patients (4%) who were positive for VGKC complex IgG (values ≥ 0.03 nmol/L). Among 316 seropositive patients evaluated clinically at our institution, 82 (26%) were seropositive for LGI1 IgG and/or CASPR2 IgG. Of these 82 patients, 27% had low (0.03-0.09 nmol/L), 51% had medium (0.10-0.99 nmol/L), and 22% had high (≥ 1.00 nmol/L) VGKC complex IgG values. Leucine-rich glioma-inactivated protein 1 IgG positivity was associated with higher VGKC complex IgG values (P< .001) and cortical presentations (P< .001); CASPR2 IgG was associated with peripheral motor excitability (P= .009). However, neither autoantibody was pathognomonic for a specific neurologic presentation or correlated significantly with cancer. Neurologic phenotypes were diverse. Cerebrocortical manifestations (including cognitive impairment and seizures) were recorded in 76% of patients with LGI1 IgG alone (n=46) and 29% with CASPR2 IgG alone (n=28). Peripheral motor hyperexcitability was found in 21% of patients with CASPR2 IgG alone and 6.5% of patients with LGI1 IgG alone. CONCLUSIONS The study emphasizes diverse and overlapping neurologic phenotypes across a range of VGKC complex IgG values and varying LGI1 IgG and CASPR2 IgG specificities. The frequent occurrence of LGI1 IgG and CASPR2 IgG in serum samples with low and medium VGKC complex IgG values supports the clinical significance of low values in clinical evaluation. Additional antigenic components of VGKC macromolecular complexes remain to be defined.
Secure protocol composition

Modular composition of security mechanisms is complicated by the way that one mechanism may reveal information that interferes with the security of another. We develop methods for modular reasoning about security protocols, using before-after assertions and protocol invariants. The before-after assertions allow us to prove properties of a sequential composition of protocol steps and therefore enable construction of complex protocols from smaller sub-protocols. Invariants provide a mechanism for ensuring that sub-protocols which are individually secure do not interact insecurely when they are composed to construct a bigger protocol. The application of the method is demonstrated by giving modular formal proofs involving two standard protocols.
Himalayan Origin and Evolution of Myricaria (Tamaricaeae) in the Neogene

Background Myricaria consists of about twelve-thirteen species and occurs in Eurasian North Temperate zone, most species in the Qinghai-Tibet Plateau (QTP) and adjacent areas. Methodology/Principal Findings Twelve species of Myricaria plus two other genera Tamarix and Reaumuria in Tamaricaceae, were sampled, and four markers, ITS, rps16, psbB-psbH, and trnL-trnF were sequenced. The relaxed Bayesian molecular clock BEAST method was used to perform phylogenetic analysis and molecular dating, and Diva, S-Diva, and maximum likelihood Lagrange were used to estimate the ancestral area. The results indicated that Myricaria could be divided into four phylogenetic clades, which correspond to four sections within the genus, of them two are newly described in this paper. The crown age of Myricaria was dated to early Miocene ca. 20 Ma, at the probable early uplifting time of the Himalayas. The Himalayas were also shown as the center of origin for Myricaria from the optimization of ancestral distribution. Migration and dispersal of Myricaria were indicated to have taken place along the Asian Mountains, including the Himalayas, Kunlun, Altun, Hendukosh, Tianshan, Altai, and Caucasus etc., westward to Europe, eastward to Central China, and northward to the Mongolian Plateau. Conclusions/Significance Myricaria spatiotemporal evolution presented here, especially the Himalayan origin at early Miocene ca. 20 Ma, and then migrated westward and eastward along the Asian mountains, offers a significant evolutionary case for QTP and Central Asian biogeography.
Sea lice as a density-dependent constraint to salmonid farming

Fisheries catches worldwide have shown no increase over the last two decades, while aquaculture has been booming. To cover the demand for fish in the growing human population, continued high growth rates in aquaculture are needed. A potential constraint to such growth is infectious diseases, as disease transmission rates are expected to increase with increasing densities of farmed fish. Using an extensive dataset from all farms growing salmonids along the Norwegian coast, we document that densities of farmed salmonids surrounding individual farms have a strong effect on farm levels of parasitic sea lice and efforts to control sea lice infections. Furthermore, increased intervention efforts have been unsuccessful in controlling elevated infection levels in high salmonid density areas in 2009–2010. Our results emphasize host density effects of farmed salmonids on the population dynamics of sea lice and suggest that parasitic sea lice represent a potent negative feedback mechanism that may limit sustainable spatial densities of farmed salmonids.
How Did the Great Recession Impact Social Preferences ? ∗

We compare behavior in modified dictators game during the “Great Recession” to behavior in otherwise identical experiments conducted amidst the economic boom that preceded it. The experiments capture both differences in indexical selfishness and differences in equalityefficiency tradeoffs. Subjects exposed to the recession exhibit higher levels of indexical selfishness and greater emphasis on efficiency relative to equality. Reproducing recessionary conditions inside the laboratory by confronting subjects with negative payoffs relative to initial endowments intensifies selfishness and increases the willingness to trade equality for efficiency, though the impact is modest relative to that of the real-world economic downturn. JEL Classification Numbers: C79, C91, D64. ∗Previously circulated as “How Does the Real World Impact Laboratory Experiments Measuring Social Preferences? Evidence from the Great Recession. ” We thank UC Berkeley Office of Planning and Analysis, Financial Aid and Scholarships Office, and Cal Answers (Student Data Warehouse) for providing administrative and survey data on our subject pool and the UC Berkeley student body. We are particularly grateful to Daniel Markovits for many thoughtful comments. We also thank James Andreoni, Colin Camerer, Syngjoo Choi, Stefano DellaVigna, John List, Ulrike Malmendier, and Matthew Rabin for helpful discussions and comments. This paper has also benefited from suggestions by the participants of seminars at several universities and conferences. †Fisman: Columbia University (email: rf250@columbia.edu); Jakiela: University of Maryland (email: pjakiela@arec.umd.edu); Kariv: University of California, Berkeley (email: kariv@berkeley.edu).
Inhibition of angiotensin converting enzyme cannot prevent increases in angiotensin II production in coronary circulation

OBJECTIVE To determine whether inhibition of angiotensin converting enzyme (ACE) can prevent angiotensin II production in the coronary circulation induced by percutaneous transluminal coronary angioplasty (PTCA) in patients with myocardial ischaemia. DESIGN, PATIENTS 41 patients who underwent elective PTCA and six control subjects who received diagnostic coronary angiography were studied. Patients were divided into two groups according to the chronic administration of ACE inhibitors (group A, 15 patients treated with ACE inhibitors; group B, 26 patients without ACE inhibitors). Blood samples were drawn through catheters placed in the aorta and coronary sinus before and 24 hours after PTCA. RESULTS Mean levels of ACE activity in the aorta were significantly lower in patients in group A than in group B. However, mean angiotensin II concentrations in the aorta were not significantly different between the two groups. Differences in basal angiotensin II concentrations between the coronary sinus and aorta, which reflected basal angiotensin II production in the coronary circulation, were not significant among group A, group B, and control subjects. The production of angiotensin II in the coronary circulation was significantly increased 24 hours after PTCA in both group A and group B to the same extent. No significant changes were observed in control subjects 24 hours after diagnostic coronary angiography. CONCLUSIONS This study revealed that inhibition of ACE activity by ACE inhibitors could not prevent increases in angiotensin II production in the coronary circulation induced by PTCA.
Endoscopy-Assisted Achilles Tendon Reconstruction With a Central Turndown Flap and Semitendinosus Augmentation

Background: The objective of this study was to report the results of a new minimally invasive Achilles reconstruction technique and to assess the perioperative morbidity, medium- to long-term outcomes, and functional results. Methods: Our series was comprised 14 patients (11 men and 3 women), with a mean age of 45.6 years at surgery. Each patient had a chronic Achilles tendon rupture. The mean interval from rupture to surgery was 5.5 months (range, 2-10). The mean total follow-up was 30.1 months (range, 12-78). All patients were operated with a central turndown flap augmented with free semitendinosus tendon graft and percutaneous sutures in a minimally invasive approach assisted by endoscopy. The patients underwent retrospective assessment by clinical examination, the American Orthopaedic Foot & Ankle Society (AOFAS) ankle and hindfoot score, and the Achilles Tendon Total Rupture Score (ATRS). Paired t tests were used to assess the preoperative and postoperative AOFAS scores, ATRS scores, and ankle range of motion. Results: The length of the defect ranged from 3 to 8 cm (mean, 5.1), while the length of the turndown flap ranged from 8 to 13 cm (mean, 10.1). The mean AOFAS score improved from 64.5 points preoperatively to 96.9 points at last follow-up. The mean ATRS score improved from 49.4 preoperatively to 91.4 points at last follow-up. None of the patients developed a wound complication. No patient had a rerupture or sural nerve damage. Conclusion: All patients in our study had a favorable outcome with no complications. We believe that with this triple-repair technique, one can achieve a strong and robust repair such as in open surgery while at the same time reducing the incidence of complications. Level of Evidence: Level III, retrospective comparative study.
OMNI scale perceived exertion at ventilatory breakpoint in children: response normalized.

PURPOSE The Children's OMNI Scale of Perceived Exertion was used to identify a response normalized rating of perceived exertion (RPE)-Overall, RPE-Legs, and RPE-Chest that corresponds to the ventilatory breakpoint (Vpt) in 8- to 12-yr-old female and male children. METHODS Subjects were a priori stratified into two fitness groups on the basis of peak oxygen uptake (VO2 peak): average (A) (41.0-49.0 mL x kg(-1) x min(-1); N = 24) and above average (AA) (50.0-58.0 mL x kg(-1) x min(-1); N = 24). Vpt was determined by a progressive cycle ergometer protocol to VO2 peak. RESULTS A gender effect was not observed for any descriptive or dependent variable. Mean VO2peak for the A group was 1.72 L x min(-1) and for the AA group 2.04 L x min(-1). Vpt corresponded to 64.0% VO2 peak for A and 74.0% VO2peak for AA. RPE-Overall (mean A and AA, 6.1), RPE-Legs (mean A and AA, 7.2), and RPE-Chest (mean A and AA, 4.5) did not differ between the fitness groups. CONCLUSION Findings indicated that undifferentiated and differentiated RPE-Vpt were similar between female and male children who varied in VO2peak and Vpt. A comparatively stable RPE-Vpt for 8- to 12-yr-old children that vary in VO2peak and Vpt indicates a group normalized perceptual response.
Probabilistic 14C Age-Depth Models Aiding the Reconstruction of Holocene Paleoenvironmental Evolution of a Marshland from Southern Hungary

ABSTRACT This paper presents first chronological results for a Holocene marshland system from the southern part of the Danube-Tisza Interfluve. Radiocarbon (14C) ages were used to build age-depth models relying of probabilistic tools. Four models have been built: a linear one using dates gained via simple calibration, a P_Sequence model, fitting a polynomial function to calibrated dates; a Gamma_Sequence considering priori given and posterior accumulation rates have been constructed. As there was no significant difference between the mean values of individual models all seem suitable for establishing a reliable chronology despite differences in 95% CI ranges. While P_Sequence models underestimated SR, values calculated from the polynomial model were not significantly different from those of the G_Sequence. Based on multiproxy geochemical, sedimentological, paleoecological data the evolution of the system was reconstructed, covering a timespan of ca. 13,000 years starting from 12,000 BC and lasting until 1300 AD. Highest accumulation rates are dated to the Early Middle Ages from the 11th century. Several climate changes could have been identified which are present in other Hungarian and Western European records too, such as the 5b IRD event at ca. 5800 BC, a humid phase around 1600 BC, and a cool humid phase around the 6th century AD.