Miracle-dz/UniFAR-FTUs huggingface dataset:
Loss of photosynthetic efficiency in the shade. An Achilles heel for the dense modern stands of our most productive C4 crops?

Abstract The wild progenitors of major C4 crops grew as individuals subjected to little shading. Today they are grown in dense stands where most leaves are shaded. Do they maintain photosynthetic efficiency in these low light conditions produced by modern cultivation? The apparent maximum quantum yield of CO2 assimilation Symbol a key determinant of light‐limited photosynthesis, has not been systematically studied in field stands of C4 crops. Symbol was derived from the initial slope of the response of leaf CO2 uptake (A) to photon flux (Q). Leaf fractional light absorptance (&agr;) was measured to determine the absolute maximum quantum yield of CO2 assimilation on an absorbed light basis Symbol Light response curves were determined on sun and shade leaves of 49 field plants of Miscanthus × giganteus and Zea mays following canopy closure. Symbol and Symbol declined significantly by 15‐27% (P<0.05) with canopy depth. Experimentally, leaf age was shown unlikely to cause this loss. Modeling canopy CO2 assimilation over diurnal courses suggested that the observed decline in Symbol with canopy depth costs 10% of potential carbon gain. Overcoming this limitation could substantially increase the productivity of major C4 crops. Symbol. No caption available. Symbol. No caption available. Symbol. No caption available. Symbol. No caption available.
Neuroglobin Ligand Binding Kinetics

Neuroglobin, cytoglobin, and hemoglobins from Drosophila melanogaster and Arabidopsis thaliana were studied for their ligand binding properties versus temperature. These globins have a common feature of being hexacoordinated (via the distal histidine) under deoxy conditions, displaying an enhanced amplitude for the alpha absorption band at 560 nm. External ligands can bind, but the transition from the hexacoordinated form to the ligand (L) bound species is slow, as expected for a replacement reaction Fe‐His ↔ Fe ↔ Fe‐L. Histidine binding is on the order of 1 ms; dissociation times are variable, and may be as long as 1 s for the highest histidine affinities. Oxygen binds rapidly but dissociates slowly, requiring as much as 1 s. These rates would correspond to a very high affinity for the pentacoordinated form; however, competition with the distal histidine leads decreases the affinity for the external ligand. The observed oxygen affinity remains in the range of 1 to 10 mm Hg. The low oxygen dissociation indicates a stabilization via H‐bonds as for certain globins from parasites (Ascaris, the trematodes). Other ligands such as CO, or CN for the ferric form, show a decreased affinity, since only the competition with the E7 histidine, but not the stabilizing H‐bond, plays a role. In addition, the competitive internal ligand leads to a weaker observed temperature dependence of the ligand affinity, since the difference in equilibrium energy for the two ligands is much lower than that of ligand binding to pentacoordinated hemoglobin. This effect could be of biological relevance for certain organisms, since it would lead to an oxygen affinity that is nearly independent of temperature. IUBMB Life, 56: 709‐719, 2004
Management of Pancreatic Fluid Collections: A Changing of the Guard from Surgery to Endoscopy

The aim of this study was to assess for any trend in management of pancreatic fluid collections (PFCs) and identify impacting factors. The endoscopy and surgical databases were queried for PFC patients. PFCs were categorized as pseudocysts (PP) or complex collections (CC) that included abscess/necrosis. The outcome measures were to compare the utilization of surgery and endoscopy from 2004 to 2007 (group I) and from 2008 to 2010 (group II) and identify factors impacting practice patterns. A total of 285 patients were treated: group I included 119 and group II 166. Of 119 group I patients, 29 per cent were treated by surgery and 71 per cent by endoscopy. Of 85 endoscopy patients, 42 per cent were drained by conventional transmural drainage and 58 per cent by endoscopic ultrasound (EUS). Of 166 group II patients, 31 per cent were treated surgically and 69 per cent endoscopically. Of the 115 endoscopy patients, 17 per cent were drained by conventional transmural drainage and 83 per cent by EUS. Compared with group I, all pseudocysts in group II were treated by endoscopy (84% vs 100%, P = 0.001). There was no difference in the rate of CC treated by endoscopy between both groups (57.7% vs 56.8%, P = 0.9). PFCs not causing luminal compression (P < 0.0001) or measuring <9 cm in size (P < 0.0001) were more likely to require EUS. There was a significant trend at our institution in the management of PFCs with all pseudocysts presently being treated only by endoscopy. The ability of EUS to access smaller size PFCs and those not causing luminal compression has significantly expanded the role of endoscopy in PFC management.
Acoustic pathways revealed: simulated sound transmission and reception in Cuvier's beaked whale (Ziphius cavirostris)

The finite element modeling (FEM) space reported here contains the head of a simulated whale based on CT data sets as well as physical measurements of sound-propagation characteristics of actual tissue samples. Simulated sound sources placed inside and outside of an adult male Cuvier's beaked whale (Ziphius cavirostris) reveal likely sound propagation pathways into and out of the head. Two separate virtual sound sources that were located at the left and right phonic lips produced beams that converged just outside the head. This result supports the notion that dual sound sources can interfere constructively to form a biologically useful and, in fact, excellent sonar beam in front of the animal. The most intriguing FEM results concern pathways by which sounds reach the ears. The simulations reveal a previously undescribed ‘gular pathway’ for sound reception in Ziphius. Propagated sound pressure waves enter the head from below and between the lower jaws, pass through an opening created by the absence of the medial bony wall of the posterior mandibles, and continue toward the bony ear complexes through the internal mandibular fat bodies. This new pathway has implications for understanding the evolution of underwater hearing in odontocetes. Our model also provides evidence for receive beam directionality, off-axis acoustic shadowing and a plausible mechanism for the long-standing orthodox sound reception pathway in odontocetes. The techniques developed for this study can be used to study acoustic perturbation in a wide variety of marine organisms.
Effects of 2‐amino‐1‐methyl‐6‐phenylimidazo[4,5‐b]pyridine on intestinal polyp development in ApcΔ716 knockout mice

Damage to the human adenomatous polyposis coli (APC) gene is responsible for not only familial adenomatous polyposis but also many sporadic cancers of the entire digestive tract. Using homologous recombination in embryonic stem cells, we recently constructed gene knockout mice with a truncation mutation in the Apc gene. These heterozygous mice developed intestinal polyps. We found that all microadenomas dissected from the earliest polyps had already lost the wild‐type allele, indicating loss of heterozygosity (LOH) (Oshima et al., Proc. Natl. Acad. Sci. USA 92:4482‐4486, 1995). Using these knockout mice, we investigated the effects of 2‐amino‐1‐methyl‐6‐phenylimidazo[4,5‐b]pyridine (PhIP), one of the most abundant heterocyclic amines found in cooked meat and fish. When PhIP was fed to these mice at 400 ppm for 8 wk, the polyp distribution shifted to a larger size range, although the total polyp number did not change significantly. Similar, but weaker, effects were observed with the other heterocyclic amines 2‐amino‐3‐methylimidazo[4,5‐f]quinoline and 2‐amino‐3,8‐dimethylimidazo[4,5‐f]quinoxaline. On the other hand, intraperitoneal injections of 2‐hydroxyamino‐1‐methyl‐6‐phenylimidazo[4,5‐b]pyridine (N‐OH‐PhIP) at a higher dose (50 mg/kg) for five consecutive days increased the polyp number significantly. This increment was not associated with mutations in the Apc gene; however, most polyps showed loss of the full‐length Apc allele (LOH). These results suggest that PhIP affects intestinal polyp development by accelerating the growth rate of microadenomas. It is also possible that high doses of N‐OH‐PhIP increase the frequency of Apc gene LOH. © 1996 Wiley‐Liss, Inc.
Polymorphism of Hassall's corpuscles in thymus of human fetuses

Background: Hassall's corpuscles (HC) are commonly used as diagnostic features for identifying human thymus and are still present in thymuses undergoing fatty degeneration in young adults. However, few studies have been performed on human fetuses. Aim: A cross-sectional study was done, to study the morphology of HC in human fetuses. Materials and Methods: Twenty-eight thymuses were collected from fetuses of gestational age ranging from 11 to 40 weeks. Thymuses were processed by paraffin embedding methods and hematoxylin and eosin staining. Results: The size of HC varied from very small (100 microns) to very large corpuscles (> 900 microns). A high level of polymorphism was also observed, from round to unusual or odd shapes corpuscles. The degenerated reticulo-epithelial cells represented the starting point in HC formation. The growth of HC was rapid, especially near 28 weeks, and the level of HC polymorphism was significantly greater after 28 weeks of gestation. In advanced stages of gestation, the increase in size of some corpuscles reduced the spaces between them, and some patterns strongly supported the hypothesis that some HC had fused in a single and larger corpuscle. Conclusion: The rapid rise in number and size of HC around 28 weeks of gestation would fit with their role in the negative selection process of thymocytes.
MR imaging of focal lung lesions: Elimination of flow and motion artifact by breath‐hold ECG‐gated and black‐blood techniques on T2‐weighted turbo SE and STIR sequences

Respiratory and cardiac motion correction may result in better turbo spin‐echo (SE) imaging of the lung. To compare breath‐hold cardiac‐gated black‐blood T2‐weighted turbo SE and turbo short‐inversion‐time inversion‐recovery (STIR) magnetic resonance (MR) imaging pulse sequences with conventional breath‐hold turbo SE and half‐Fourier acquisition single‐shot turbo spin‐echo (HASTE) sequences for lesion conspicuity of focal lung lesions, 42 patients with focal lung lesions were prospectively studied with MR imaging at 1.5 T. Helical computed tomography was used as a reference. In comparison with the conventional breath‐hold turbo SE sequence, all black‐blood sequences had fewer image artifacts arising from the heart and blood flow. The overall image quality for the black‐blood turbo SE and turbo STIR sequences was superior to that for the breath‐hold turbo SE and HASTE sequence (P < 0.01). Not only focal lung lesions but also surrounding inflammatory changes were clearly visualized with these two sequences. With the HASTE sequence, although several slices could be obtained in one breath‐hold, both the tumor and vessels appeared blurred. We conclude that T2‐weighted turbo SE and turbo STIR imaging of the lung with effective suppression of flow and motion artifacts provide high‐quality images in patients with focal lung lesions. J. Magn. Reson. Imaging 1999;9:691–698. © 1999 Wiley‐Liss, Inc.
Hardware and software innovations in energy-efficient system-reliability monitoring

Many threats that can undermine the reliability of a system can be realized at design, while others only during its online operation. As the availability of system monitoring sensors and run-time software increases in heterogeneous platforms, there is a demand for a novel platform-independent framework that can capture and deliver, in a holistic way, system level self-assessment and adaptation capabilities at run-time. In this paper, two groups from academia and one from industry present the following three contributions. First, system reliability is considered from the perspective of novel timing guardband designs for aging mitigation. Effective timing guardband models are presented from the physical to the system level, while targeting multiple wear-out mechanisms. Second, a technique for correlating complex software and micro-architectural events with power integrity loss is presented. The presented technique uses an embedded voltage noise sensor, a power-network model and a genetic algorithm for identifying workload that triggers power-network resonances which can ultimately lead to system failures. Third, the ‘PRiME’ cross-layer programming framework is presented that unites available sensors and dynamic-voltage and frequency scaling actuators with learning-based run-time process mapping and scheduling algorithms. Scenarios on exploring the energy efficiency and reliability of heterogeneous platforms using run-time software derived from the developed framework are also reviewed.
The Importance of Overhydration in Determining Peritoneal Dialysis Technique Failure and Patient Survival in Anuric Patients

Purpose Loss of residual renal function (RRF) is associated with an increased risk for peritoneal dialysis (PD) technique failure and patient death. We wished to determine which factors were associated with PD technique failure and patient mortality once urine output had fallen to <100 mL/day. Methods We followed 183 PD patients who lost RRF and who had measurements taken at that time of PD small solute clearances, ultrafiltration volume, PD transport status and multiple frequency bioelectrical impedance assessments (MFBIA) of extracellular water (ECW). Results Results: 119 (65%) patients had PD technique failure or died during a median follow-up of 20.8 (10.5–36) months. This group had more men (58.8% vs. 31.9%, p = 0.011), and were older 57.9 ± 14.7 vs. 49.3 years (p = 0.002). These patients had a higher median C-reactive protein 5.5 [4.8–8.2] vs (5.0 [2–6] p = 0.013), and greater comorbidity (Davies grade 1 [0–1] vs. 0[0–1], p<0.001, and a higher ratio of ECW/TBW (0.45 ± 0.07 vs 0.42 ± 0.04, p<0.001). There were no differences in icodextrin usage, small solute clearance or ultrafiltration volumes. On multivariate Cox regression, ECW excess was significantly associated with PD technique failure and patient survival (β 1.09, p<0.001 and β1.17, p = 0.005), respectively. Conclusions Loss of urine output requires PD to provide both adequate solute clearances and volume control. We found that PD technique failure and patient death were associated with ECW excess. Prospective interventional studies are required to determine whether correction of volume status improves PD patient outcomes.
Identification of a lipopolysaccharide α‐2,3‐sialyltransferase from Haemophilus influenzae

We have identified a gene for the addition of N‐acetylneuraminic acid (Neu5Ac) in an α‐2,3‐linkage to a lactosyl acceptor moiety of the lipopolysaccharide (LPS) of the human pathogen Haemophilus influenzae. The gene is one that was identified previously as a phase‐variable gene known as lic3A. Extracts of H. influenzae, as well as recombinant Escherichia coli strains producing Lic3A, demonstrate sialyltransferase activity in assays using synthetic fluorescent acceptors with a terminal galactosyl, lactosyl or N‐acetyl‐lactosaminyl moiety. In the RM118 strain of H. influenzae, Lic3A activity is modulated by the action of another phase‐variable glycosyltransferase, LgtC, which competes for the same lactosyl acceptor moiety. Structural analysis of LPS from a RM118:lgtC mutant and the non‐typeable strain 486 using mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy confirmed that the major sialylated species has a sialyl‐α‐(2–3)‐lactosyl extension off the distal heptose. This sialylated glycoform was absent in strains containing a lic3A gene disruption. Low amounts of sialylated higher molecular mass glycoforms were present in RM118:lgtC lic3A, indicating the presence of a second sialyltransferase. Lic3A mutants of H. influenzae strains show reduced resistance to the killing effects of normal human serum. Lic3A, encoding an α‐2,3‐sialyltransferase activity, is the first reported phase‐variable sialyltransferase gene.
The growth of nerves in relation to the formation of premuscle cell masses in the developing chick forelimb

A description is given of the growth of segmental nerves 13 to 16 (SN13 to SN16) from the brachial myotomes into the ventral and dorsal premuscle cell masses of the chick forelimb. At stage 25 (Hamburger and Hamilton, 1951), segmental nerves have converged to form two nerve trunks which enter the ventral and dorsal premuscle cell masses. These nerves grow into the limb, parallel to its proximodistal axis. The nerve trunk in the ventral compartment, the brachialis longus inferior (bli n), grows on the brachial artery as far as the metacarpals. The nerve trunk in the dorsal compartment, the brachialis longus superior (bls n), grows on the precartilage adjacent to a dorsal premuscle density as far as the metacarpals.
Determination of α‐synuclein concentration in human plasma using ELISA

The nerve cell protein α‐synuclein is important in Parkinson's disease and dementia with Lewy bodies, and its expression levels are directly linked to development of the diseases. Quantification of the plasma level of α‐synuclein may therefore be important as a biomarker for disease susceptibility. We present a quantitative measurement of α‐synuclein in the plasma of healthy control subjects in relation to their age using a novel enzyme‐linked immunosorbent assay (ELISA). The plasma concentration among the 44 blood donors displayed a median of 5.6 µg/L (range 2.1–19.4 µg/L) with a narrow distribution (25 % and 75 % percentiles, 4.0 and 7.2 µg/L) and there was no correlation with age and gender. This narrow concentration range and the ease of measuring the quantitative ELISA support future investigations of plasma α‐synuclein in relation to neurodegenerative diseases.
Investigation of a microwave pulse compressor with a Magic-tee-based plasma interference switch

A microwave pulse compressor with a Magic-tee as an interference switch was investigated in numerical simulations and experimentally. If the compressor cavity is connected to the H- or E-arm of the Magic-tee with shorted side arms, the necessary condition for the microwave energy storage is the identicalness of the shorted arms regardless of the frequency. It means that the compressor operation in different cavity eigenfrequencies is possible without mechanical tuning. We have studied the two-frequency S-band compressor. Two characteristic geometries corresponding to different regimes of the microwave energy accumulation and release were tested using input pulses of 200-400 kW power, 2.4 μs duration, and variable frequency, 2.8 to 2.9 GHz. The geometries are characterized by an RF electric field in the interference switch that is higher or lower than the field in the cavity. For both geometries, the nanosecond output pulses in two resonant frequencies were obtained; the maximal peak output power measured was ~1.8 MW. The efficiency of the microwave extraction was limited by either an insufficient coupling to the tee output arm (in the case of a high field in the tee) or non-uniformity of the plasma discharge (in the case of low field in the tee).
Synthesis and Analysis of Double-Input Single-Output DC/DC Converters

This paper describes a systematic procedure using power flow graphs for generating all possible double-input single-output (DISO) dc/dc converters. To maximize the generality of applications, the input ports can possibly be connected with voltage source(s) or current source(s), and the output port can be connected with a voltage load or current load. The control methods are described in this paper. A DISO converter with two voltage sources and one voltage load is taken as an example to analyze a few key properties of practical relevance, including input voltage range, efficiency, power distribution, and switching stress. A popular application of DISO converters involves the use of a battery as storage element, and for this specific case, possible choices for the converters, the control method, and the attainable efficiency are discussed. Finally, experimental results are presented to verify the analytical results.
Peri-implantitis in partially edentulous patients: association with inadequate plaque control.

OBJECTIVE The aim of the present study was to describe some clinical periodontal features of partially edentulous patients referred for the treatment of peri-implantitis. MATERIAL AND METHODS The 23 subjects involved in this study were selected from consecutive patients referred to the department of Periodontology Södra Alvsborgs Hospital, Borås, Sweden, for treatment of peri-implantitis during 2006. The patients had clinical signs of peri-implantitis around one or more dental implants (i.e.>or=6 mm pockets, bleeding on pockets and/or pus and radiographic images of bone loss to>or=3 threads of the implants) and remaining teeth in the same and/or opposite jaw. The following clinical variables were recorded: Plaque Index (PI), Gingival Bleeding Index (GBI) Probing Pocket Depth (PPD), Access/capability to oral hygiene at implant site (yes/no), Function Time. The patients were categorized in the following sub-groups: Periodontitis/No periodontitis, Bone loss/No bone loss at teeth, Smoker/Non-smokers. RESULTS Out of the 23 patients, the majority (13) had minimal bone loss at teeth and no current periodontitis; 5 had bone loss at teeth exceeding 1/3 of the length of the root but not current periodontitis and only 5 had current periodontitis. Six patients were smokers (i.e. smoking more than 10 cig/day). The site level analysis showed that only 17 (6%) of the 281 teeth present had >or=1 pocket of >or=6mm, compared to 58 (53%) of the total 109 implants (28 ITI and 81 Brånemark); 74% of the implants had no accessibility to proper oral hygiene. High proportion of implants with diagnosis of peri-implantitis were associated with no accessibility/capability for appropriate oral hygiene measures, while accessibility/capability was rarely associated with peri-implantitis. Indeed 48% of the implants presenting peri-implantitis were those with no accessibility/capability for proper oral hygiene (65% positive predict value) with respect to 4% of the implants with accessibility/capability (82% negative predict value). CONCLUSION The results of the study indicate that local factors such as accessibility for oral hygiene at the implant sites seems to be related to the presence or absence of peri-implantitis. Peri-implantitis was a frequent finding in subjects having signs of minimal loss of supporting bone around the remaining natural dentition and no signs of presence of periodontitis (i.e. presence of periodontal pockets of >or=6 mm at natural teeth). Only 6 of the examinated subjects were smokers. In view of these results we should like to stress the importance of giving proper oral hygiene instructions to the patients who are rehabilitated with dental implant and of proper prosthetic constructions that allow accessibility for oral hygiene around implants.