jimnoneill/paper-to-field-training huggingface dataset:
Screening for GARS Variants in A Cohort of Chinese Patients With Inherited Peripheral Neuropathy

Field: Medicine (Health Sciences)

Abstract Background CMT2D is a rare subtype of axonal CMT, caused by the mutation of glycyl-tRNA synthetase (GARS) gene which is also a disease-causing gene of distal spinal muscular atrophy type V (dSMA-V) or hereditary motor neuropathy 5A (HMN5A). There were only several case reports in China, and no epidemiological study of CMT2D/ HMN5A yet. Methods We recruited the patients of Chinese Han descent clinically diagnosed with inherited peripheral neuropathy (IPN) from the Department of Neurology at Chinese PLA General Hospital (Beijing, China) from December 20, 2012 to July 31, 2019. All patients underwent a detailed medical history, neurological examination, laboratory examination, electrophysiological studies, and genetic testing. Results A total of 206 unrelated patients underwent genetic analysis, and we found four mutations of GARS from four different families, including c.794C>T (p.S265F), c.374A>G (p.E125G), c.1000A>T (p.I334F) and c.781T>G (p.Y261D), the first three of them were considered pathogenic. As for the three pathogenic mutation carriers, one patient was diagnosed as CMT2D, two patients were diagnosed as HMN5A. Conclusion GARS mutation is a rare cause of inherited peripheral neuropathy and the phenotype tends to be CMT2D or HMN5A. There might be a relatively higher mutation frequency in Asian population compared with Caucasians. Combination of clinical phenotype, auxiliary tests and genetic evidence to assess the pathogenicity of genetic variants in patients suspected as IPN is of vital importance.
Effect of temperature and light on growth of planktic green algae isolated from Lake Hovsgol, Mongolia

Field: Agricultural and Biological Sciences (Life Sciences)

Four species of planktic green algae, Oocystella mongolica, Monoraphidium contortum, Pseudodidymocystis planctonica and Closterium parvulum were isolated from the ancient ultraoligotrophic Lake Hovsgol, Mongolia. While O. mongolica is considered to be an endemic species of the lake, the others are cosmopolitan species. Lake Hovsgol freezes between November and May, and the maximum water temperature in the pelagic area is ca. 14°C in summer. In order to clarify the growth characteristics on temperature and light of the strains, culture experiments were conducted. Although these algae live in cold habitats, the optimum temperatures for growth of the strains were 20-25 °C under high light conditions. All strains could grow at 5 °C, which was the lowest temperature examined, and showed their best growth rate at 10°C under the lowest light conditions (10 μmol photons m -2 . s -1 The results of culture experiments were discussed with regard to their natural habitats.
Organization vs Disorganization: A Computational Model of Goals, Motivation and Problem Solving

Field: Computer Science (Physical Sciences)

This paper presents an agent-based simulation of “disorganization” and its effect on problem solving. The Prime objective of the simulation is to determine the variance in problem solving under two settings. The first has inflexible structural limitations enacted on the agents (organization) while the other has very little structural limitations (disorganization). The simulation also employs goals as a foundation for the motivation with which agents solve problems. Findings of the simulation show that the “organization” setting guarantees a minimal number of problems are solved independent of how much simulated employees interact with each other. Instead, the “disorganization” setting seems to be more efficient when agents extend the range of social interaction, in or outside their working group, department, or division.
Single molecule fluorescence imaging of biosensors, ribozymes and molecular spiders

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Single molecule fluorescence imaging has been developed in recent times to expand our understanding of the heterogeneity and biological mechanisms of molecular ensembles. In this dissertation, such imaging techniques, along with ensemble fluorescence spectroscopy tools have been used to investigate three systems of nucleic acid enzymes. An engineered biosensor built from a theophylline aptamer and the hammerhead ribozyme (termed an aptazyme) was scrutinized using single molecule fluorescence resonance energy transfer (smFRET) and ensemble fluorescence studies. It was found that a catalytically active state is accessed both in the theophylline-bound and, if less frequently, in the ligand-free state. The resultant residual activity (leakage) in the absence of theophylline contributes to the limited dynamic range (<100 fold) observed for the aptazyme. In addition, slow conformational rearrangements dampen the speed in which the catalytically active conformation is accessed. In contrast, the only known naturally occurring aptazyme uses a chemical cofactor to instantaneously trigger catalysis (with a 100,000 fold activation range), rather than the slower rearrangement of an inactive into an active structure. To examine the effects of the U-turn of the hepatitis delta virus (HDV) ribozyme, recently found to be at the heart of the ribozyme’s catalytic core, both DNA and RNA ligase mediated methods were evaluated to assemble the ribozyme from chemical synthesized fragments. Upon successful assembly of the ribozyme, preliminary smFRET studies were performed revealing global dynamics and heterogeneity promising to unveil new insight into the functional role of the U-turn. Recently designed nano-robots called Molecular Spiders use nucleic acid enzymes as “fuel” to traverse on a specific two-dimensional landscape. In this thesis, individual Spider movement was surveyed by single fluorescent particle tracking. Two-dimensional Spider movement was followed in real-time, providing evidence for the previously hypothesized model that Spiders move in a self-repellent autonomous (cybernetic) walk. These nano-walkers represent potential drug delivery vehicles with the ability to understand and follow external cues. Overall, the work presented in this dissertation has illuminated the suitability of single particle fluorescence techniques to monitor the functional behavior and heterogeneity of single nucleic-acid based molecules ranging from biosensors and small catalytic ribozymes to novel molecular nano-robots.
Widespread introgression of Solatium phureja DNA in potato (S. tuberosum) dihaploids

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract Dihaploids were assumed to be of parthenogenic origin but cv. ‘Pentland Crown’ dihaploids produced at the Scottish Crop Research Institute (SCRI), Dundee, Scotland, are known to contain DNA from the S. phureja dihaploid inducer. This study investigates whether inducer DNA occurs in dihaploids of cultivars ‘Aminca’, ‘Brio’, ‘Lizen’ and ‘Sirtema’, produced at INRA, Ploudaniel, France. Two microsatellite markers and five simple sequence repeat 5′‐anchored polymerase chain reaction (PCR) primers were used to generate markers. Markers originating from the dihaploid inducer were detected in 13 of the 19 INRA dihaploids and in some dihaploids from each cultivar. Greater introgression occurred in ‘Lizen’ dihaploids than in ‘Brio’ dihaploids, suggesting that the female ( S. tuberosum ) parent influences introgression. The percentage of INRA dihaploids containing inducer DNA was similar to that for ‘Pentland Crown’ dihaploids (c. 65%). The micro‐satellite markers provided the first evidence of the transfer of specific, potentially useful, genes from the inducer to the dihaploid offspring. Interspecific introgression during dihaploid induction is more widespread than previously thought and researchers should be aware that it may influence the results of research using dihaploids.
162 HFREF WITH IMPROVED EJECTION FRACTION AFTER CORONARY ARTERY BYPASS GRAFT (CABG) AND REVERSE REMODELING PREDICTOR FACTORS

Field: Medicine (Health Sciences)

Abstract Background The purpose of this study is [1] to evaluate the incidence of heart failure with improved ejection fraction (HFimpEF) in patients with reduced ejection fraction (HFrEF, EF&lt;40%) undergoing surgical myocardial revascularization via coronary artery bypass graft (CABG), [2] to identify predictor factors for improved ejection fraction and [3] to study overall survival between the two populations, i.e. patients with improved EF (i.e. impEF) versus patients with non-improved EF (i.e. non-impEF). Methods N=699 patients, admitted between January 2000 and December 2020, were selected from the Cardiac Surgery database of our facility and analyzed retrospectively. The selection criteria for this study were [1] having EF&lt;40% at the time of surgery and [2] undergoing coronary artery bypass surgery. Patients were evaluated at preoperative baseline, immediate post-operative, 3-months follow up, 1-year follow-up and the last available follow-up. ImpEF was defined as EF&gt;40% and at least 10% EF points improvement at 1-3 months follow-up. We assessed the incidence of improved Ejection Fraction (impEF) after surgical revascularization at 3-months follow-up, defined as the improvement of Ejection Fraction from a baseline LVEF of ≤40% to a new LVEF &gt;40%, within a measurable improvement of ≥10 points of percentage from baseline EF; predictors of impEF were investigated and the association between impEF and mortality risk was finally explored. Results At 3-months follow-up, 221 patients were evaluated and the 42.5% (n=94) of these showed impEF. BMI, LVESVi and LVEF were predictors of impEF at multivariable analysis. ImpEF was significantly associated with better long-term survival in our cohort. Conclusions In patients with reduced EF undergoing surgical myocardial revascularization, impEF occurs in 42.5% of cases within 3 months and is associated with better overall survival. The predictors of impEF identified in this study might be helpful in the definition of patients at higher probability of impEF before surgery.
Georges Scelle’s Study of the Slave Trade: French Solidarism Revisited

Field: Arts and Humanities (Social Sciences)

<it>In 1906, Georges Scelle defended his state thesis in the Faculty of Law at the University of Paris. The young scholar had taken upon himself to study the history of the transatlantic slave trade from a legal and political perspective. The result is a monumental work, in which Scelle traces the evolution of the ‘</it>asientos de negros<it>’ – that is, the agreements that the Spanish crown signed with an individual, a company or another sovereign by which the latter was granted the privilege (and often the monopoly) to supply African slaves to the Spanish colonies in the Americas. Scelle’s thesis offers us an opportunity to explore the meaning and ambivalences of a certain left sensibility in our discipline. How did a radical left international lawyer respond to slavery and human exploitation at the turn of the 20th century? In particular, how did the vocabulary of solidarity and freedom play out when analysing the commercial enterprise that epitomized the most exploitative form of globalization?</it>
Effect of Translational Signals on mRNA Decay in Bacillus subtilis

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

ABSTRACT A 254-nucleotide model mRNA, designated Δ ermC mRNA, was used to study the effects of translational signals and ribosome transit on mRNA decay in Bacillus subtilis . Δ ermC mRNA features a strong ribosome-binding site (RBS) and a 62-amino-acid-encoding open reading frame, followed by a transcription terminator structure. Inactivation of the RBS or the start codon resulted in a fourfold decrease in the mRNA half-life, demonstrating the importance of ternary complex formation for mRNA stability. Data for the decay of Δ ermC mRNAs with stop codons at positions increasingly proximal to the translational start site showed that actual translation—even the formation of the first peptide bond—was not important for stability. The half-life of an untranslated 3.2-kb Δ ermC - lacZ fusion RNA was similar to that of a translated Δ ermC - lacZ mRNA, indicating that the translation of even a longer RNA was not required for wild-type stability. The data are consistent with a model in which ribosome binding and the formation of the ternary complex interfere with a 5′-end-dependent activity, possibly a 5′-binding endonuclease, which is required for the initiation of mRNA decay. This model is supported by the finding that increasing the distance from the 5′ end to the start codon resulted in a 2.5-fold decrease in the mRNA half-life. These results underscore the importance of the 5′ end to mRNA stability in B . subtilis .
Latest Trend of Industrial Network Security Standards and Vendor Activities

Field: Engineering (Physical Sciences)

As end-users' demands of integrating plant information with enterprise information increase, more industrial automation and control system (IA&CS) networks are required to be connected to corporate network. According to this trend, "IA&CS security" is becoming much more important than ever. However, there are many cases where normal IT security method can not be applied without modification because of the characteristics of IA&CS network, such as different data management priority and variation of equipments. To solve this problem there are many activities going on. This paper introduces a couple of standardization activities together with vendor activities to solve this problem
[A long-term follow-up of a patient with DIDMOAD (Wolfram) syndrome].

Field: Medicine (Health Sciences)

A 19-year-old Japanese woman developed diabetes mellitus, diabetes insipidus and optic atrophy. Other abnormal ocular findings included color blindness, elevated dark adaptation threshold and constriction of visual fields. Diabetic retinopathy, which is considered to be rare in this syndrome, also was found in the fundi of this patient. During the nine-year follow-up period, diabetic retinopathy deteriorated despite treatment by photocoagulation and vitrectomy, suggesting the importance of ophthalmological examinations in patients with DIDMOAD syndrome.
Salmonella typhimurium için serotip spesifik dna işaretleyicisinin rapd-pcr metodu ile tanısı.

Field: Immunology and Microbiology (Life Sciences)

This study was performed for the identification of specific DNA marker using RAPD-PCR (Random Amplified Polymorphic DNA) method for serotype Salmonella Typhimurium which is one of the most prevalent serotype causing food poisining all over the world. The Primer 3 (RAPD 9.1), 5̕-CGT GCA CGC-3ء, was used in RAPD-PCR with 35 different Salmonella isolates. 12 of them were serotype Salmonella Typhimurium and 23 of them were belonging to other six different serotypes. Accordingly, two different 300 bp and 700 bp sized amplification products were obtained from the 12 different Salmonella Typhimurium isolates. On the other hand, other 23 Salmonella isolates of six different serotypes gave only 300 bp amplification band while 700 bp amplification band was not observed with Primer 3 (RAPD 9.1). After the discovery of 700 bp fragmentwhich was specific for S. Typhimurium, it was decided to sequence. The 700 bp band was ligated onto the vector pUC 19 to sequence. The cloninig operation gave positive results by the formation of blue and white colonies, but plasmid isolation process from white colonies containing the ligated vector was not achieved. Therefore, sequencing of the 700 bp fragment together with plasmid DNA could not be completed. However it wil be sent to USA for sequencing. According to these results, it was discovered that 700 bp amplification product was found as a specific polymorphic region for Salmonella Typhimurium after RAPD application on genomic DNA and this band can be used as a specific marker for detection and identification of Salmonella Typhimurium.
Maximal dimensional subalgebras of general Cartan‐type Lie algebras

Field: Mathematics (Physical Sciences)

Abstract Let be a field of characteristic zero and let be the general Cartan‐type Lie algebra. In this paper, we study Lie subalgebras of of maximal Gelfand–Kirillov (GK) dimension, that is, with . For , we completely classify such , proving a conjecture of the second author. As a corollary, we obtain a new proof that satisfies the Dixmier conjecture, in other words, , a result first shown by Du. For arbitrary , we show that if is a GK‐dimension subalgebra of , then is not (left or right) noetherian.
LHD 9O-BC01-01-NF #189111.1

Field: Physics and Astronomy (Physical Sciences)

The plasma monitor cameras are installed in 6-T, 6-O and 10-O ports for monitoring LHD plasmas. Five cameras are set in 3-O port for observing the lower divertor structure near 2.5-L port and the plasma-wall interactions on the divertor plates.
Successful surgical treatment of rupture of coronary arteriovenous fistula with unconsciousness after chest and back pain.

Field: Medicine (Health Sciences)

A 65 year-old woman was admitted to our hospital, because of unconsciousness after chest and back pain. Echocardiography showed pericardial effusion. She suffered from pre-shock due to cardiac tamponade. Although a cause of cardiac tamponade was unclear, we performed emergency surgical treatment without coronary angiography. In operation, we found a rupture of coronary arteriovenous fistula and repaired it. The patient recovered from the surgery uneventfully. Coronary artery fistula is an abnormal communication between a coronary artery and a cardiac chamber or major vessel. It is the most common congenital anomalies of the coronary arteries. Many patients with these anomalies remain asymptomatic, but some patients develop symptoms of congestive heart failure, infective endocarditis, myocardial ischemia, arrhythmia, or rupture of an aneurismal fistula. Usually, the dilatation of fistula is common, and although 19% of this may become aneurysmal, the rupture of the aneurysm is very rare. We report a case of ruptured coronary arteriovenous fistula who underwent successful emergent surgery.
Genomic Variability of O Islands Encoding Tellurite Resistance in Enterohemorrhagic Escherichia coli O157:H7 Isolates

Field: Immunology and Microbiology (Life Sciences)

ABSTRACT Strains of Escherichia coli causing enterohemorrhagic colitis belonging to the O157:H7 lineage are reported to be highly related. Fifteen strains of E. coli O157:H7 and 1 strain of E. coli O46:H − (nonflagellated) were examined for the presence of potassium tellurite resistance (Te r ). Te r genes comprising terABCDEF were shown previously to be part of a pathogenicity island also containing integrase, phage, and urease genes. PCR analysis, both conventional and light cycler based, demonstrated that about one-half of the Te r E. coli O157:H7 strains (6 of 15), including the Sakai strain, which has been sequenced, carried a single copy of the Te r genes. Five of the strains, including EDL933, which has also been sequenced, contained two copies. Three other O157:H7 strains and the O46:H − strain did not contain the Te r genes. In strains containing two copies, the Te r genes were associated with the serW and serX tRNA genes. Five O157:H7 strains resembled the O157 Sakai strain whose sequence contained one copy, close to serX , whereas in one isolate the single copy was associated with serW . There was no correlation between Te r and the ability to produce Shiga toxin ST1 or ST2. The Te r MIC for most strains, containing either one or two copies, was 1,024 μg/ml, although for a few the MIC was intermediate, 64 to 128 μg/ml, which could be increased to 512 μg/ml by pregrowth of strains in subinhibitory concentrations of potassium tellurite. Reverse transcriptase PCR analysis confirmed that in most strains Te r was constitutive but that in the rest it was inducible and involved induction of terB and terC genes. Only the terB , - C , - D , and - E genes are required for Te r . The considerable degree of homology between the ter genes on IncH12 plasmid R478, which originated in Serratia marcescens , and pTE53, from an E. coli clinical isolate, suggests that the pathogenicity island was acquired from a plasmid. This work demonstrates diversity among E. coli O157:H7 isolates, at least as far as the presence of Te r genes is concerned.
Drilling a Blind-Entry 4,000-ft Horizontal Well in a Depleted Sandstone Reservoir

Field: Engineering (Physical Sciences)

ABSTRACT Phillips drilled a 4000' horizontal oil well at 6048' true vertical depth in a depleted (1 Ib/gal equivalent mud weight) sandstone reservoir in Caddo Co., Oklahoma, to combat gas coning problems. Seven external casing packers were set in the slotted liner for production control. Initial production from the well was 1800 barrels of oil per day (BOPD) with little gas.
Wide-angle and high-efficiency acoustic retroreflectors enabled by many-objective optimization algorithm and deep learning models

Field: Engineering (Physical Sciences)

By redirecting the incident wave energy back toward the source or sensor, retroreflectors mitigate signal losses, render a higher signal-to-noise transmission with improved sensing performance, and are highly desirable in acoustic applications such as remote sensing and detection, medical ultrasound imaging, and underwater communications. In this paper, we propose a different and efficient approach to realize a wide-angle high-efficiency retroreflector that is based on the design frame of acoustic metagrating. By integrating a many-objective optimization algorithm with a deep learning neural network, we construct a comprehensive and efficient optimization framework to intelligently design the metagrating so that its seven different diffraction orders work synergistically to realize the intended high-efficiency retroreflection functionality over a broad and continuous range of incident angles. Compared with the existing approaches based on corner cubes, Luneburg lenses, or dual-layer metasurfaces, the single-layer configuration of the retroreflector has a relatively simple unit-cell structure and can be easily extended to higher working frequencies. Both the proposed design paradigm itself and the high-performance retroreflector configuration may find applications in various scenarios including ultrasonic detection and imaging, music performance monitoring, and underwater communications.
ECO-3D: Equivariant Contrastive Learning for Pre-training on Perturbed 3D Point Cloud

Field: Computer Science (Physical Sciences)

In this work, we investigate contrastive learning on perturbed point clouds and find that the contrasting process may widen the domain gap caused by random perturbations, making the pre-trained network fail to generalize on testing data. To this end, we propose the Equivariant COntrastive framework which closes the domain gap before contrasting, further introduces the equivariance property, and enables pre-training networks under more perturbation types to obtain meaningful features. Specifically, to close the domain gap, a pre-trained VAE is adopted to convert perturbed point clouds into less perturbed point embedding of similar domains and separated perturbation embedding. The contrastive pairs can then be generated by mixing the point embedding with different perturbation embedding. Moreover, to pursue the equivariance property, a Vector Quantizer is adopted during VAE training, discretizing the perturbation embedding into one-hot tokens which indicate the perturbation labels. By correctly predicting the perturbation labels from the perturbed point cloud, the property of equivariance can be encouraged in the learned features. Experiments on synthesized and real-world perturbed datasets show that ECO-3D outperforms most existing pre-training strategies under various downstream tasks, achieving SOTA performance for lots of perturbations.