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Article Commentary Clinical Case Study
Cilie C. van ‘t Klooster , Jan J. Uil , Joep van der Leeuw , Elaine F. Eppens , Susanne C. Marczinski
DOI: 10.1373/clinchem.2016.267823 Published November 2017
Cilie C. van ‘t Klooster
Ziekenhuis Gelderse Vallei, Ede, the Netherlands.
Jan J. Uil
Ziekenhuis Gelderse Vallei, Ede, the Netherlands.
Joep van der Leeuw
Ziekenhuis Gelderse Vallei, Ede, the Netherlands.
Elaine F. Eppens
Ziekenhuis Gelderse Vallei, Ede, the Netherlands.
Susanne C. Marczinski
Ziekenhuis Gelderse Vallei, Ede, the Netherlands.

A 46-year-old man, originally from Iran, with no relevant medical history, was admitted with intermittent acute colic pain in the lower abdomen with nausea and vomiting over the past few weeks. On physical examination, the patient had lower abdominal pain without guarding. Laboratory findings showed a microcytic anemia, a heterozygote β-thalassemia, mild leukocytosis, and slight liver enzyme activity increases ( Table 1 , case 1). Hepatitis, cytomegalovirus, and Epstein–Barr virus were negative. Ultrasonography and computed tomography scan of the abdomen did not suggest liver, kidney, or pancreas disease, and gastroscopy and colonoscopy revealed no pathology. The patient denied substance abuse. The symptoms improved spontaneously and the patient awaited further diagnostics in the outpatient clinic. Within 1 week, the patient returned with similar symptoms. Acute intermittent porphyria (AIP) 2 was suspected and urine porphyrins were measured. Urine δ-aminolevulinic acid (ALA) concentration was increased at 96.9 mmol/mol of creatinine (reference interval <3.9 mmol/mol creatinine), porphobilinogen (PBG) concentration was normal at 8 μmol/L (reference interval 0–9 μmol/L), and coproporphyrinogen III concentration was increased at 91.8 nmol/mmol of creatinine (reference interval 2.9–19.3 nmol/mmol of creatinine). These findings excluded the diagnosis AIP, as the PBG concentrations remained normal and both ALA concentration and coproporphyrinogen III concentrations increased.

View this table:
Table 1.

Biochemical and hematological findings in the described cases.

Another 42-year-old man, originally from Iran and with no relevant medical history, presented with similar complaints of acute diffuse colic abdominal pain with nausea and vomiting. He complained of diffuse abdominal pain without guarding. Laboratory findings showed microcytic anemia, without signs of iron deficiency or thalassemia; basophilic stippling of red blood cells; mild leukocytosis; and increased liver enzyme activities ( Table 1 , case 2). Viral serology was negative. The patient denied substance abuse. Considering a gastric ulcer, a gastroscopy was performed that showed no abnormalities. Doppler ultrasonography of the abdomen was negative for liver, kidney, or pancreas disease, or mesenteric ischemia. On the basis of the symptoms, porphyrin analysis was performed, with the following results: ALA concentration was increased at 79.6 mmol/mol of creatinine and the free erythrocyte protoporphyrin concentration was also increased at 126.3 μg/dL (reference interval 0–65 μg/dL). The patient's gums revealed Burton's lines. Unknown to the medical team at the time, the 2 patients were friends.

Phase relations among muscles or MN activities are commonly used in pattern-generation studies to aid in deciphering the circuit's architecture from its motor output. Here we used the standard deviations of phase differences between MN bursts recorded from different nerves and hemiganglia as manifestations of the strength of coupling between the different underlying oscillatory networks. Our estimation was based on the assumption that strong coupling results in low variability in the phase relations between the oscillators, and vice versa ( Sale Finishline collarless shirt White Aspesi Footlocker Finishline Cheap Price Clearance Outlet Get To Buy For Sale Sale Clearance Store NM9B7f2M
; Greene and Spirito, 1979 ; Rillich et al., 2013 ). For every pair of MNs, five bouts were sampled from each of five different preparations ( N =5 animals, n =25 bouts, except for L2Dep:R3Lev: N =3, n =15). To obtain the variability between the selected pairs of MNs, we first calculated the centre-of-gravity (CoG, defined in Materials and methods) of the MN bursts and then the standard deviation of the phase difference between CoGs, separately for each recording bout. Fig.6 A summarizes these standard deviations, and TableS4 summarizes the significance tests among the different groups.

Fig. 6.

Phase relations and phase-locking. (A) Scheme of phase relations s.d., as a measure of coupling strength. Arrow end, levator; round end, depressor; circular connection, coupling between antagonistic MNs within a single hemiganglion. Solid and dashed lines represent pairs of in-phase and anti-phase MN pairs, respectively. Lower s.d. indicates stronger coupling. Endogenous coupling strength was found to be dependent upon these parameters: (i) direction, ipsilateral coupling is stronger than contralateral and diagonal coupling; (ii) hemiganglia involved, contralateral coupling differs between ganglia; and (iii) function of the coupled MNs, coupling between levator and depressor is stronger than between two levators. (B) Phase-locking strength between mesothoracic and metathoracic MNs is asymmetrical and stronger in the ascending pathway. Data for three pairs are normally distributed (Shapiro-Wilk test,  > 0.05) and are presented. Line, box, and whiskers represent mean, s.e.m. and s.d., respectively. Significance level is marked as *<0.05. Transition phase-lock is stronger in the ascending pathway for each of the pairs. Asymmetric phase-locking indicates differences in the mechanisms of coordination in different directions.

We first examined phase relations and found a left-right symmetry in coupling strength, allowing the pooling of data (e.g. mean phase and variability of R2Lev:R3Lev and L2Lev:L3Lev did not differ, nor did those of L2Lev:R2Dep and R2Lev:L2Dep). Coupling between antagonist pairs within a hemiganglion was found to be similar in the meso- and metathorax and significantly stronger than coupling between different hemiganglia (Mann–Whitney test, P <0.05) for all but L2Dep:L3Lev. Inter-hemiganglia coupling of Lev-Dep pairs was found to be greater than that of Lev-Lev pairs. In a comparison between pairs of similar function in different hemiganglia, ipsilateral coupling was found to be stronger than contralateral and diagonal coupling (Mann–Whitney test, P <0.05). Moreover, metathoracic coupling was found to be stronger than mesothoracic coupling (Mann–Whitney test, P =0.044). We found no significant differences between contralateral and diagonal coupling.

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The development of computational tools to describe and analyze microbial communities is in a “Red Queen”-type race where advances in computational power are met with expansions in sequencing capacity and vice versa. As the length and number of reads multiply, data analysis resources must meet the challenge. Although mothur goes a long way toward making data analysis efficient, flexible, and simple, the analyses are by no means trivial, and researchers must take care to ensure that their experiments are well designed and thought out and that their results are biologically plausible. The field of microbial ecology is experiencing an amazing revolution where we can now design experiments with sophisticated experimental designs. Tools such as mothur open new possibilities so that the primary limitation is our imagination.

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Funding for mothur has been provided by the College of Natural Resources and the Environment at the University of Massachusetts, a grant from the Sloan Foundation, a grant from the National Science Foundation (award 0743432), and the Austrian GEN-AU project BIN.

We appreciate the input and support of the more than 900 users who registered their use of DOTUR, SONS, ∫-LIBSHUFF, or TreeClimber over the past 5 years.

P.D.S. conceived, designed, and prepared the manuscript; P.D.S., S.L.W., T.R., and G.G.T. generated source code; and P.D.S., S.L.W., T.R., J.R.H., M.H., E.B.H., R.A.L., B.B.O., D.H.P., C.J.R., J.W.S., B.S., D.J.V., and C.F.W. provided documentation. All authors helped in the final editing of the manuscript.

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If the CPU is M-class this is all that needs to be done since the architecture itself is designed in such a way that functions obeying the normal AAPCS ABI constraints are valid exception handlers.

If the CPU is not M-class, the prologue and epilogue are modified to save all non-banked registers that are used, so that upon return the user-mode state will not be corrupted. Note that to avoid unnecessary overhead, only general-purpose (integer) registers are saved in this way. If VFP operations are needed, that state must be saved manually.

Specifically, interrupt kinds other than “FIQ” will save all core registers except “lr” and “sp”. “FIQ” interrupts will save r0-r7.

If the CPU is not M-class, the return instruction is changed to one of the canonical sequences permitted by the architecture for exception return. Where possible the function itself will make the necessary “lr” adjustments so that the “preferred return address” is selected.

Unfortunately the compiler is unable to make this guarantee for an “UNDEF” handler, where the offset from “lr” to the preferred return address depends on the execution state of the code which generated the exception. In this case a sequence equivalent to “movs pc, lr” will be used.

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Clang supports the GNU style attribute on AVR targets. This attribute may be attached to a function definition and instructs the backend to generate appropriate function entry/exit code so that it can be used directly as an interrupt service routine.

On the AVR, the hardware globally disables interrupts when an interrupt is executed. The first instruction of an interrupt handler declared with this attribute is a SEI instruction to re-enable interrupts. See also the signal attribute that does not insert a SEI instruction.

interrupt (MIPS)

Clang supports the GNU style attribute on MIPS targets. This attribute may be attached to a function definition and instructs the backend to generate appropriate function entry/exit code so that it can be used directly as an interrupt service routine.

By default, the compiler will produce a function prologue and epilogue suitable for an interrupt service routine that handles an External Interrupt Controller (eic) generated interrupt. This behaviour can be explicitly requested with the “eic” argument.

Otherwise, for use with vectored interrupt mode, the argument passed should be of the form “vector=LEVEL” where LEVEL is one of the following values: “sw0”, “sw1”, “hw0”, “hw1”, “hw2”, “hw3”, “hw4”, “hw5”. The compiler will then set the interrupt mask to the corresponding level which will mask all interrupts up to and including the argument.

The semantics are as follows:

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is used to mark a function in RenderScript.

In RenderScript, functions are used to express data-parallel computations. The RenderScript runtime efficiently parallelizes functions to run on computational resources such as multi-core CPUs and GPUs. See the RenderScript documentation for more information.

long_call (gnu::long_call, gnu::far)

Clang supports the , , and attributes on MIPS targets. These attributes may only be added to function declarations and change the code generated by the compiler when directly calling the function. The attribute allows calls to the function to be made using the instruction, which requires the function to be located in the same naturally aligned 256MB segment as the caller. The and attributes are synonyms and require the use of a different call sequence that works regardless of the distance between the functions.

These attributes have no effect for position-independent code.

These attributes take priority over command line switches such as and .

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Clang supports the GNU style and attributes on MIPS targets. These attributes may be attached to a function definition and instructs the backend to generate or not to generate microMIPS code for that function.

These attributes override the and options on the command line.

Use this attribute to indicate that the specified function has no caller-saved registers. That is, all registers are callee-saved except for registers used for passing parameters to the function or returning parameters from the function. The compiler saves and restores any modified registers that were not used for passing or returning arguments to the function.

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